1
|
Pan H, Wei L, Zhao H, Xiao Y, Li Z, Ding H. Perception of the Biocontrol Potential and Palmitic Acid Biosynthesis Pathway of Bacillus subtilis H2 through Merging Genome Mining with Chemical Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4834-4848. [PMID: 38401001 DOI: 10.1021/acs.jafc.3c06411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2024]
Abstract
Bacillus has been widely studied for its potential to protect plants from pathogens. Here, we report the whole genome sequence of Bacillus subtilis H2, which was isolated from the tea garden soil of Guiyang Forest Park. Strain H2 showed a broad spectrum of antagonistic activities against many plant fungal pathogens and bacteria pathogens, including the rice blast fungus Magnaporthe oryzae, and showed a good field control effect against rice blast. The complete genome of B. subtilis H2 contained a 4,160,635-bp circular chromosome, with an average G + C content of 43.78%. Through the genome mining of strain H2, we identified 7 known antimicrobial compound biosynthetic gene clusters (BGCs) including sporulation killing factor, surfactin, bacillaene, fengycin, bacillibactin, subtilosin A, and bacilysin. Palmitic acid (PA), a secondary metabolite, was detected and identified in the H2 strain through genome mining analysis and gas chromatography-mass spectrometry (GC-MS). Additionally, we propose, for the first time, that the type II fatty acid synthesis (FAS) pathway in Bacillus is responsible for PA biosynthesis. This finding was confirmed by studying the antimicrobial activity of PA and conducting reverse transcription-quantitative polymerase chain reaction (RT-qPCR) experiments. We also identified numerous genes associated with plant-bacteria interactions in the H2 genome, including more than 94 colonization-related genes, more than 34 antimicrobial genes, and more than 13 plant growth-promoting genes. These findings contribute to our understanding of the biocontrol mechanisms of B. subtilis H2 and have potential applications in crop disease control.
Collapse
Affiliation(s)
- Hang Pan
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou, China
| | - Longfeng Wei
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou, China
| | - Hao Zhao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou, China
| | - Yang Xiao
- Institution of Supervision and Inspection Product Quality of Guizhou Province, Guiyang 550004, China
| | - Zhu Li
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, Guizhou, China
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Haixia Ding
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang 550025, China
| |
Collapse
|
2
|
Cronan JE. Unsaturated fatty acid synthesis in bacteria: Mechanisms and regulation of canonical and remarkably noncanonical pathways. Biochimie 2024; 218:137-151. [PMID: 37683993 PMCID: PMC10915108 DOI: 10.1016/j.biochi.2023.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/02/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
Unsaturated phospholipid acyl chains are required for membrane function in most bacteria. The double bonds of the cis monoenoic chains arise by two distinct pathways depending on whether oxygen is required. The oxygen-independent pathway (traditionally called the anaerobic pathway) introduces the cis double bond by isomerization of the trans double bond intermediate of the fatty acid elongation cycle. Double bond isomerization occurs at an intermediate chain length (e.g., C10) and the isomerization product is elongated to the C16-C18 chains that become phospholipid monoenoic acyl chains. This pathway was first delineated in Escherichia coli and became the paradigm pathway. However, studies of other bacteria show deviations from this paradigm, the most exceptional being reversal of the fatty acid elongation cycle by a reaction paralleling the initial step in the β-oxidative degradation of fatty acids. In the oxygen-dependent pathway diiron enzymes called desaturases introduce a double bond into a saturated acyl chain by regioselective cis dehydrogenation through activation of molecular oxygen with an active-site diiron cluster. This difficult hydrogen abstraction from a methylene group often occurs at the midpoint of a saturated fatty acyl chain. In bacteria the acyl chain is a phospholipid acyl chain, and the desaturase is membrane bound. Both the oxygen-independent oxygen-dependent pathways are transcriptionally regulated by repressor and activator proteins that respond to small molecule ligands such as acyl-CoAs. However, in Bacillus subtilis the desaturase is synthesized only at low growth temperatures, a process controlled by a signal transduction regulatory pathway dependent on membrane lipid properties.
Collapse
Affiliation(s)
- John E Cronan
- Departments of Microbiology and Biochemistry, University of Illinois, Urbana, 61801, USA.
| |
Collapse
|
3
|
Linney JA, Routledge SJ, Connell SD, Larson TR, Pitt AR, Jenkinson ER, Goddard AD. Identification of membrane engineering targets for increased butanol tolerance in Clostridium saccharoperbutylacetonicum. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184217. [PMID: 37648011 DOI: 10.1016/j.bbamem.2023.184217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/17/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023]
Abstract
There is a growing interest in the use of microbial cell factories to produce butanol, an industrial solvent and platform chemical. Biobutanol can also be used as a biofuel and represents a cleaner and more sustainable alternative to the use of conventional fossil fuels. Solventogenic Clostridia are the most popular microorganisms used due to the native expression of butanol synthesis pathways. A major drawback to the wide scale implementation and development of these technologies is the toxicity of butanol. Various membrane properties and related functions are perturbed by the interaction of butanol with the cell membrane, causing lower yields and higher purification costs. This is ultimately why the technology remains underemployed. This study aimed to develop a deeper understanding of butanol toxicity at the membrane to determine future targets for membrane engineering. Changes to the lipidome in Clostridium saccharoperbutylacetonicum N1-4 (HMT) throughout butanol fermentation were investigated with thin layer chromatography and mass spectrometry. By the end of fermentation, levels of phosphatidylglycerol lipids had increased significantly, suggesting an important role of these lipid species in tolerance to butanol. Using membrane models and in vitro assays to investigate characteristics such as permeability, fluidity, and swelling, it was found that altering the composition of membrane models can convey tolerance to butanol, and that modulating membrane fluidity appears to be a key factor. Data presented here will ultimately help to inform rational strain engineering efforts to produce more robust strains capable of producing higher butanol titres.
Collapse
Affiliation(s)
- John A Linney
- School of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Sarah J Routledge
- School of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Simon D Connell
- School of Physics and Astronomy and The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Tony R Larson
- Department of Biology, University of York, York YO10 5DD, UK
| | - Andrew R Pitt
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | | | - Alan D Goddard
- School of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
| |
Collapse
|
4
|
Ramón A, Esteves A, Villadóniga C, Chalar C, Castro-Sowinski S. A general overview of the multifactorial adaptation to cold: biochemical mechanisms and strategies. Braz J Microbiol 2023; 54:2259-2287. [PMID: 37477802 PMCID: PMC10484896 DOI: 10.1007/s42770-023-01057-4] [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: 03/20/2023] [Accepted: 06/29/2023] [Indexed: 07/22/2023] Open
Abstract
Cold environments are more frequent than people think. They include deep oceans, cold lakes, snow, permafrost, sea ice, glaciers, cold soils, cold deserts, caves, areas at elevations greater than 3000 m, and also artificial refrigeration systems. These environments are inhabited by a diversity of eukaryotic and prokaryotic organisms that must adapt to the hard conditions imposed by cold. This adaptation is multifactorial and includes (i) sensing the cold, mainly through the modification of the liquid-crystalline membrane state, leading to the activation of a two-component system that transduce the signal; (ii) adapting the composition of membranes for proper functions mainly due to the production of double bonds in lipids, changes in hopanoid composition, and the inclusion of pigments; (iii) producing cold-adapted proteins, some of which show modifications in the composition of amino acids involved in stabilizing interactions and structural adaptations, e.g., enzymes with high catalytic efficiency; and (iv) producing ice-binding proteins and anti-freeze proteins, extracellular polysaccharides and compatible solutes that protect cells from intracellular and extracellular ice. However, organisms also respond by reprogramming their metabolism and specifically inducing cold-shock and cold-adaptation genes through strategies such as DNA supercoiling, distinctive signatures in promoter regions and/or the action of CSPs on mRNAs, among others. In this review, we describe the main findings about how organisms adapt to cold, with a focus in prokaryotes and linking the information with findings in eukaryotes.
Collapse
Affiliation(s)
- Ana Ramón
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Adriana Esteves
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Carolina Villadóniga
- Laboratorio de Biocatalizadores Y Sus Aplicaciones, Facultad de Ciencias, Instituto de Química Biológica, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Cora Chalar
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Susana Castro-Sowinski
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay.
- Laboratorio de Biocatalizadores Y Sus Aplicaciones, Facultad de Ciencias, Instituto de Química Biológica, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay.
| |
Collapse
|
5
|
Yu YH, Chen C, Ma JR, Zhang YY, Yan MF, Zhang WB, Hu Z, Wang HH, Ma JC. The FabA-FabB Pathway Is Not Essential for Unsaturated Fatty Acid Synthesis but Modulates Diffusible Signal Factor Synthesis in Xanthomonas campestris pv. campestris. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:119-130. [PMID: 36515967 DOI: 10.1094/mpmi-09-22-0182-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Most bacteria use type II fatty acid synthesis (FAS) systems for synthesizing fatty acids, of which the conserved FabA-FabB pathway is considered to be crucial for unsaturated fatty acid (UFA) synthesis in gram-negative bacteria. Xanthomonas campestris pv. campestris, the phytopathogen of black rot disease in crucifers, produces higher quantities of UFAs under low-temperature conditions for increasing membrane fluidity. The fabA and fabB genes were identified in the X. campestris pv. campestris genome by BLAST analysis; however, the growth of the X. campestris pv. campestris fabA and fabB deletion mutants was comparable to that of the wild-type strain in nutrient and minimal media. The X. campestris pv. campestris ΔfabA and ΔfabB strains produced large quantities of UFAs and, altogether, these results indicated that the FabA-FabB pathway is not essential for growth or UFA synthesis in X. campestris pv. campestris. We also observed that the expression of X. campestris pv. campestris fabA and fabB restored the growth of the temperature-sensitive Escherichia coli fabA and fabB mutants CL104 and CY242, respectively, under non-permissive conditions. The in-vitro assays demonstrated that the FabA and FabB proteins of X. campestris pv. campestris catalyzed FAS. Our study also demonstrated that the production of diffusible signal factor family signals that mediate quorum sensing was higher in the X. campestris pv. campestris ΔfabA and ΔfabB strains and greatly reduced in the complementary strains, which exhibited reduced swimming motility and attenuated host-plant pathogenicity. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
- Yong-Hong Yu
- Guangdong Food and Drug Vocational College, Guangzhou, Guangdong 510520, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Cheng Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Jian-Rong Ma
- Guangdong Food and Drug Vocational College, Guangzhou, Guangdong 510520, China
| | - Yuan-Yin Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Ming-Feng Yan
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Wen-Bin Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Zhe Hu
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Hai-Hong Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Jin-Cheng Ma
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| |
Collapse
|
6
|
Chen A, Mindrebo JT, Davis TD, Kim WE, Katsuyama Y, Jiang Z, Ohnishi Y, Noel JP, Burkart MD. Mechanism-based cross-linking probes capture the Escherichia coli ketosynthase FabB in conformationally distinct catalytic states. Acta Crystallogr D Struct Biol 2022; 78:1171-1179. [PMID: 36048156 PMCID: PMC9435599 DOI: 10.1107/s2059798322007434] [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: 04/12/2022] [Accepted: 07/20/2022] [Indexed: 11/10/2022] Open
Abstract
Ketosynthases (KSs) catalyse essential carbon-carbon bond-forming reactions in fatty-acid biosynthesis using a two-step, ping-pong reaction mechanism. In Escherichia coli, there are two homodimeric elongating KSs, FabB and FabF, which possess overlapping substrate selectivity. However, FabB is essential for the biosynthesis of the unsaturated fatty acids (UFAs) required for cell survival in the absence of exogenous UFAs. Additionally, FabB has reduced activity towards substrates longer than 12 C atoms, whereas FabF efficiently catalyses the elongation of saturated C14 and unsaturated C16:1 acyl-acyl carrier protein (ACP) complexes. In this study, two cross-linked crystal structures of FabB in complex with ACPs functionalized with long-chain fatty-acid cross-linking probes that approximate catalytic steps were solved. Both homodimeric structures possess asymmetric substrate-binding pockets suggestive of cooperative relationships between the two FabB monomers when engaged with C14 and C16 acyl chains. In addition, these structures capture an unusual rotamer of the active-site gating residue, Phe392, which is potentially representative of the catalytic state prior to substrate release. These structures demonstrate the utility of mechanism-based cross-linking methods to capture and elucidate conformational transitions accompanying KS-mediated catalysis at near-atomic resolution.
Collapse
Affiliation(s)
- Aochiu Chen
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jeffrey T. Mindrebo
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Tony D. Davis
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Woojoo E. Kim
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yohei Katsuyama
- Department of Biotechnology, The Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ziran Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yasuo Ohnishi
- Department of Biotechnology, The Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Joseph P. Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| |
Collapse
|
7
|
Zheng Y, Zhou X, Wang C, Zhang J, Chang D, Liu W, Zhu M, Zhuang S, Shi H, Wang X, Chen Y, Cheng Z, Lin Y, Nan L, Sun Y, Min L, Liu J, Chen J, Zhang J, Huang M. Effect of Tanshinone IIA on Gut Microbiome in Diabetes-Induced Cognitive Impairment. Front Pharmacol 2022; 13:890444. [PMID: 35899118 PMCID: PMC9309808 DOI: 10.3389/fphar.2022.890444] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/09/2022] [Indexed: 01/14/2023] Open
Abstract
Diabetes-induced cognitive impairment (DCI) presents a major public health risk among the aging population. Previous clinical attempts on known therapeutic targets for DCI, such as depleted insulin secretion, insulin resistance, and hyperglycaemia have delivered poor patient outcomes. However, recent evidence has demonstrated that the gut microbiome plays an important role in DCI by modulating cognitive function through the gut–brain crosstalk. The bioactive compound tanshinone IIA (TAN) has shown to improve cognitive and memory function in diabetes mellitus models, though the pharmacological actions are not fully understood. This study aims to investigate the effect and underlying mechanism of TAN in attenuating DCI in relation to regulating the gut microbiome. Metagenomic sequencing analyses were performed on a group of control rats, rats with diabetes induced by a high-fat/high-glucose diet (HFD) and streptozotocin (STZ) (model group) and TAN-treated diabetic rats (TAN group). Cognitive and memory function were assessed by the Morris water maze test, histopathological assessment of brain tissues, and immunoblotting of neurological biomarkers. The fasting blood glucose (FBG) level was monitored throughout the experiments. The levels of serum lipopolysaccharide (LPS) and tumor necrosis factor-α (TNF-α) were measured by enzyme-linked immunoassays to reflect the circulatory inflammation level. The morphology of the colon barrier was observed by histopathological staining. Our study confirmed that TAN reduced the FBG level and improved the cognitive and memory function against HFD- and STZ-induced diabetes. TAN protected the endothelial tight junction in the hippocampus and colon, regulated neuronal biomarkers, and lowered the serum levels of LPS and TNF-α. TAN corrected the reduced abundance of Bacteroidetes in diabetic rats. At the species level, TAN regulated the abundance of B. dorei, Lachnoclostridium sp. YL32 and Clostridiodes difficile. TAN modulated the lipid metabolism and biosynthesis of fatty acids in related pathways as the main functional components. TAN significantly restored the reduced levels of isobutyric acid and butyric acid. Our results supported the use of TAN as a promising therapeutic agent for DCI, in which the underlying mechanism may be associated with gut microbiome regulation.
Collapse
Affiliation(s)
- Yanfang Zheng
- Fujian Key Laboratory of Chinese Materia Medica, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Xian Zhou
- NICM Health Research Institute, Western Sydney University, Westmead, NSW, Australia
| | - Chenxiang Wang
- Fujian Key Laboratory of Chinese Materia Medica, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Jialin Zhang
- College of Integrated Traditional Chinese and Western Medicine, Fu Jian University of Traditional Chinese Medicine, Fu Zhou, China
| | - Dennis Chang
- NICM Health Research Institute, Western Sydney University, Westmead, NSW, Australia
| | - Wenjing Liu
- Fujian Key Laboratory of Chinese Materia Medica, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - MingXing Zhu
- College of Traditional Chinese, Fu Jian University of Traditional Chinese Medicine, Fu Zhou, China
| | - Shuting Zhuang
- College of Integrated Traditional Chinese and Western Medicine, Fu Jian University of Traditional Chinese Medicine, Fu Zhou, China
| | - Hong Shi
- College of Integrated Traditional Chinese and Western Medicine, Fu Jian University of Traditional Chinese Medicine, Fu Zhou, China
| | - Xiaoning Wang
- College of Integrated Traditional Chinese and Western Medicine, Fu Jian University of Traditional Chinese Medicine, Fu Zhou, China
| | - Yong Chen
- College of Integrated Traditional Chinese and Western Medicine, Fu Jian University of Traditional Chinese Medicine, Fu Zhou, China
| | - Zaixing Cheng
- Fujian Key Laboratory of Chinese Materia Medica, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Yanxiang Lin
- Fujian Key Laboratory of Chinese Materia Medica, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Lihong Nan
- Fujian Key Laboratory of Chinese Materia Medica, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Yibin Sun
- Fujian Key Laboratory of Chinese Materia Medica, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Li Min
- College of Traditional Chinese, Fu Jian University of Traditional Chinese Medicine, Fu Zhou, China
| | - Jin Liu
- Fujian Key Laboratory of Chinese Materia Medica, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Jianyu Chen
- Fujian Key Laboratory of Chinese Materia Medica, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- *Correspondence: Jianyu Chen, ; Jieping Zhang, ; Mingqing Huang,
| | - Jieping Zhang
- College of Integrated Traditional Chinese and Western Medicine, Fu Jian University of Traditional Chinese Medicine, Fu Zhou, China
- *Correspondence: Jianyu Chen, ; Jieping Zhang, ; Mingqing Huang,
| | - Mingqing Huang
- Fujian Key Laboratory of Chinese Materia Medica, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- *Correspondence: Jianyu Chen, ; Jieping Zhang, ; Mingqing Huang,
| |
Collapse
|
8
|
Chen A, Jiang Z, Burkart MD. Enzymology of standalone elongating ketosynthases. Chem Sci 2022; 13:4225-4238. [PMID: 35509474 PMCID: PMC9006962 DOI: 10.1039/d1sc07256k] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/09/2022] [Indexed: 12/16/2022] Open
Abstract
The β-ketoacyl-acyl carrier protein synthase, or ketosynthase (KS), catalyses carbon-carbon bond formation in fatty acid and polyketide biosynthesis via a decarboxylative Claisen-like condensation. In prokaryotes, standalone elongating KSs interact with the acyl carrier protein (ACP) which shuttles substrates to each partner enzyme in the elongation cycle for catalysis. Despite ongoing research for more than 50 years since KS was first identified in E. coli, the complex mechanism of KSs continues to be unravelled, including recent understanding of gating motifs, KS-ACP interactions, substrate recognition and delivery, and roles in unsaturated fatty acid biosynthesis. In this review, we summarize the latest studies, primarily conducted through structural biology and molecular probe design, that shed light on the emerging enzymology of standalone elongating KSs.
Collapse
Affiliation(s)
- Aochiu Chen
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Ziran Jiang
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| |
Collapse
|
9
|
Dong H, Ma J, Chen Q, Chen B, Liang L, Liao Y, Song Y, Wang H, Cronan JE. A cryptic long-chain 3-ketoacyl-ACP synthase in the Pseudomonas putida F1 unsaturated fatty acid synthesis pathway. J Biol Chem 2021; 297:100920. [PMID: 34181948 PMCID: PMC8319022 DOI: 10.1016/j.jbc.2021.100920] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/08/2021] [Accepted: 06/23/2021] [Indexed: 11/30/2022] Open
Abstract
The Pseudomonas putida F1 genome contains five genes annotated as encoding 3-ketoacyl-acyl carrier protein (ACP) synthases. Four are annotated as encoding FabF (3-ketoacyl-ACP synthase II) proteins, and the fifth is annotated as encoding a FabB (3-ketoacyl-ACP synthase I) protein. Expression of one of the FabF proteins, FabF2, is cryptic in the native host and becomes physiologically important only when the repressor controlling fabF2 transcription is inactivated. When derepressed, FabF2 can functionally replace FabB, and when expressed from a foreign promoter, had weak FabF activity. Complementation of Escherichia coli fabB and fabF mutant strains with high expression showed that P. putida fabF1 restored E. coli fabF function, whereas fabB restored E. coli fabB function and fabF2 restored the functions of both E. coli fabF and fabB. The P. putida ΔfabF1 deletion strain was almost entirely defective in synthesis of cis-vaccenic acid, whereas the ΔfabB strain is an unsaturated fatty acid (UFA) auxotroph that accumulated high levels of spontaneous suppressors in the absence of UFA supplementation. This was due to increased expression of fabF2 that bypasses loss of fabB because of the inactivation of the regulator, Pput_2425, encoded in the same operon as fabF2. Spontaneous suppressor accumulation was decreased by high levels of UFA supplementation, whereas competition by the P. putida β-oxidation pathway gave increased accumulation. The ΔfabB ΔfabF2 strain is a stable UFA auxotroph indicating that suppressor accumulation requires FabF2 function. However, at low concentrations of UFA supplementation, the ΔfabF2 ΔPput_2425 double-mutant strain still accumulated suppressors at low UFA concentrations.
Collapse
Affiliation(s)
- Huijuan Dong
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jincheng Ma
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Qunyi Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Bo Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Lujie Liang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yuling Liao
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yulu Song
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Haihong Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China.
| | - John E Cronan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
| |
Collapse
|
10
|
Zhang F, Li Z, Zhou J, Gu Y, Tan X. Comparative study on fruit development and oil synthesis in two cultivars of Camellia oleifera. BMC PLANT BIOLOGY 2021; 21:348. [PMID: 34301189 PMCID: PMC8299657 DOI: 10.1186/s12870-021-03114-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The oil-tea tree (Camellia oleifera Abel.) is a woody tree species that produces edible oil in the seed. C. oleifera oil has high nutritional value and is also an important raw material for medicine and cosmetics. In China, due to the uncertainty on maturity period and oil synthesis mechanism of many C. oleifera cultivars, growers may harvest fruits prematurely, which could not maximize fruit and oil yields. In this study, our objective was to explore the mechanism and differences of oil synthesis between two Camellia oleifera cultivars for a precise definition of the fruit ripening period and the selection of appropriate cultivars. RESULTS The results showed that 'Huashuo' had smaller fruits and seeds, lower dry seed weight and lower expression levels of fatty acid biosynthesis genes in July. We could not detect the presence of oil and oil bodies in 'Huashuo' seeds until August, and oil and oil bodies were detected in 'Huajin' seeds in July. Moreover, 'Huashuo' seeds were not completely blackened in October with up to 60.38% of water and approximately 37.98% of oil in seed kernels whose oil content was much lower than normal mature seed kernels. The oil bodies in seed endosperm cells of 'Huajin' were always higher than those of 'Huashuo' from July to October. CONCLUSION Our results confirmed that C. oleifera 'Huashuo' fruits matured at a lower rate compared to 'Huajin' fruits and that 'Huajin' seeds entered the oil synthesis period earlier than 'Huashuo' seeds. Moreover, 'Huashuo' fruits did not mature during the Frost's Descent period (October 23-24 each year).
Collapse
Affiliation(s)
- Fanhang Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Ze Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forestry Industry of Hunan Province, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
| | - Junqin Zhou
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forestry Industry of Hunan Province, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
| | - Yiyang Gu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forestry Industry of Hunan Province, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
- Engineering Technology Research Center of Southern Hilly and Mountainous Ecological Non-Wood Forestry Industry of Hunan Province, Central South University of Forestry and Technology, Changsha, 410004 Hunan China
| |
Collapse
|
11
|
Mindrebo JT, Chen A, Kim WE, Re RN, Davis TD, Noel JP, Burkart MD. Structure and Mechanistic Analyses of the Gating Mechanism of Elongating Ketosynthases. ACS Catal 2021; 11:6787-6799. [DOI: 10.1021/acscatal.1c00745] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Jeffrey T. Mindrebo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Aochiu Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Woojoo E. Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Rebecca N. Re
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Tony D. Davis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| | - Joseph P. Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, California 92037, United States
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, United States
| |
Collapse
|
12
|
Jingjing E, Lili M, Zichao C, Rongze M, Qiaoling Z, Ruiyin S, Zongbai H, Junguo W. Effects of buffer salts on the freeze-drying survival rate of Lactobacillus plantarum LIP-1 based on transcriptome and proteome analyses. Food Chem 2020; 326:126849. [DOI: 10.1016/j.foodchem.2020.126849] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/16/2020] [Accepted: 04/17/2020] [Indexed: 10/24/2022]
|
13
|
Nature and bioprospecting of haloalkaliphilics: a review. World J Microbiol Biotechnol 2020; 36:66. [DOI: 10.1007/s11274-020-02841-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 04/14/2020] [Indexed: 01/07/2023]
|
14
|
Combating tigecycline resistant Acinetobacter baumannii: A leap forward towards multi-epitope based vaccine discovery. Eur J Pharm Sci 2019; 132:1-17. [DOI: 10.1016/j.ejps.2019.02.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/31/2019] [Accepted: 02/16/2019] [Indexed: 01/27/2023]
|
15
|
Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level. Sci Rep 2019; 9:1371. [PMID: 30718562 PMCID: PMC6362236 DOI: 10.1038/s41598-018-37679-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/13/2018] [Indexed: 01/16/2023] Open
Abstract
Clostridium beijerinckii NRRL B-598 is a sporulating, butanol and hydrogen producing strain that utilizes carbohydrates by the acetone-butanol-ethanol (ABE) fermentative pathway. The pathway consists of two metabolic phases, acidogenesis and solventogenesis, from which the latter one can be coupled with sporulation. Thorough transcriptomic profiling during a complete life cycle and both metabolic phases completed with flow cytometry, microscopy and a metabolites analysis helped to find out key genes involved in particular cellular events. The description of genes/operons that are closely involved in metabolism or the cell cycle is a necessary condition for metabolic engineering of the strain and will be valuable for all C. beijerinckii strains and other Clostridial species. The study focused on glucose transport and catabolism, hydrogen formation, metabolic stress response, binary fission, motility/chemotaxis and sporulation, which resulted in the composition of the unique image reflecting clostridial population changes. Surprisingly, the main change in expression of individual genes was coupled with the sporulation start and not with the transition from acidogenic to solventogenic metabolism. As expected, solvents formation started at pH decrease and the accumulation of butyric and acetic acids in the cultivation medium.
Collapse
|
16
|
Jenkins SV, Vang KB, Gies A, Griffin RJ, Jun SR, Nookaew I, Dings RPM. Sample storage conditions induce post-collection biases in microbiome profiles. BMC Microbiol 2018; 18:227. [PMID: 30591021 PMCID: PMC6307155 DOI: 10.1186/s12866-018-1359-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/28/2018] [Indexed: 01/12/2023] Open
Abstract
Background Here we investigated the influence of different stabilization and storage strategies on the quality and composition of the fecal microbial community. Namely, same-day isolated murine DNA was compared to samples stored for 1 month in air at ambient temperature, with or without preservative buffers (i.e. EDTA and lysis buffer), different temperatures (i.e. 4 °C, − 20 °C, and − 80 °C), and hypoxic conditions. Results Only storage in lysis buffer significantly reduced DNA content, yet without integrity loss. Storage in EDTA affected alpha diversity the most, which was also reflected in cluster separation. Distinct changes were also seen in the phyla and bacterial species abundance per storage strategy. Metabolic function analysis showed 22 pathways not significantly affected by storage conditions, whereas the tyrosine metabolism pathway was significantly changed in all strategies except by EDTA. Conclusion Each long-term storage strategy introduced a unique post-collection bias, which is important to take into account when interpreting data. Electronic supplementary material The online version of this article (10.1186/s12866-018-1359-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Samir V Jenkins
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Kieng B Vang
- Center for Integrative Nanotechnology Sciences, University of Arkansas, Little Rock, AR, USA
| | - Allen Gies
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Robert J Griffin
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Se-Ran Jun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ruud P M Dings
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| |
Collapse
|
17
|
Suppression of fabB Mutation by fabF1 Is Mediated by Transcription Read-through in Shewanella oneidensis. J Bacteriol 2016; 198:3060-3069. [PMID: 27573012 DOI: 10.1128/jb.00463-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 08/20/2016] [Indexed: 12/19/2022] Open
Abstract
As type II fatty acid synthesis is essential for the growth of Escherichia coli, its many components are regarded as potential targets for novel antibacterial drugs. Among them, β-ketoacyl-acyl carrier protein (ACP) synthase (KAS) FabB is the exclusive factor for elongation of the cis-3-decenoyl-ACP (cis-3-C10-ACP). In our previous study, we presented evidence to suggest that this may not be the case in Shewanella oneidensis, an emerging model gammaproteobacterium renowned for its respiratory versatility. Here, we identified FabF1, another KAS, as a functional replacement for FabB in S. oneidensis In fabB+ or desA+ (encoding a desaturase) cells, which are capable of making unsaturated fatty acids (UFA), FabF1 is barely produced. However, UFA auxotroph mutants devoid of both fabB and desA genes can be spontaneously converted to suppressor strains, which no longer require exogenous UFAs for growth. Suppression is caused by a TGTTTT deletion in the region upstream of the fabF1 gene, resulting in enhanced FabF1 production. We further demonstrated that the deletion leads to transcription read-through of the terminator for acpP, an acyl carrier protein gene immediately upstream of fabF1 There are multiple tandem repeats in the region covering the terminator, and the TGTTTT deletion, as well as others, compromises the terminator efficacy. In addition, FabF2 also shows an ability to complement the FabB loss, albeit substantially less effectively than FabF1. IMPORTANCE It has been firmly established that FabB for UFA synthesis via type II fatty acid synthesis in FabA-containing bacteria such as E. coli is essential. However, S. oneidensis appears to be an exception. In this bacterium, FabF1, when sufficiently expressed, is able to fully complement the FabB loss. Importantly, such a capability can be obtained by spontaneous mutations, which lead to transcription read-through. Therefore, our data, by identifying the functional overlap between FabB and FabFs, provide new insights into the current understanding of KAS and help reveal novel ways to block UFA synthesis for therapeutic purposes.
Collapse
|
18
|
Diederich AK, Duda KA, Romero-Saavedra F, Engel R, Holst O, Huebner J. Deletion of fabN in Enterococcus faecalis results in unsaturated fatty acid auxotrophy and decreased release of inflammatory cytokines. Innate Immun 2016; 22:284-93. [PMID: 27009913 DOI: 10.1177/1753425916639669] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 02/17/2016] [Indexed: 01/09/2023] Open
Abstract
The Gram-positive bacterium Enterococcus faecalis can cause life-threatening infections and is resistant to several commonly used antibiotics. The type II fatty acid pathway in bacteria is discussed as a potential target for antimicrobial therapy. However, it was shown that inhibition or deletion of its enzymes can be rescued in Gram-positive bacteria by supplementation with fatty acids. Here we show that by deletion of the fabN gene, which is essential for unsaturated fatty acid (UFA) synthesis in E. faecalis, growth is impaired but can be rescued by supplementation with oleic acid or human serum. Nonetheless, we demonstrate alterations of the UFA profile after supplementation with oleic acid in the ΔfabN mutant using a specific glycolipid. In addition, we demonstrate that cytokine release in vitro is almost abolished after stimulation of mouse macrophages by the mutant in comparison to the wild type. The results indicate that fabN is not a suitable target for antimicrobials as UFA auxotrophy can be overcome. However, deletion of fabN resulted in a decreased inflammatory response indicating that fabN and resulting UFA synthesis are relevant for virulence.
Collapse
Affiliation(s)
- Ann-Kristin Diederich
- Center for Infectious Disease and Travel Medicine, University Medical Center Freiburg, Freiburg, Germany Division of Pediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany Department of Microbiology, Faculty of Biology, Albert-Ludwigs-University, Freiburg, Germany
| | - Katarzyna A Duda
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Priority Area Asthma & Allergy, Research Center Borstel, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), D-23845 Borstel, Germany
| | - Felipe Romero-Saavedra
- Center for Infectious Disease and Travel Medicine, University Medical Center Freiburg, Freiburg, Germany 2EA4655 U2RM Stress/Virulence, University of Caen Lower-Normandy, Caen, France
| | - Regina Engel
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Priority Area Asthma & Allergy, Research Center Borstel, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), D-23845 Borstel, Germany
| | - Otto Holst
- Division of Structural Biochemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Priority Area Asthma & Allergy, Research Center Borstel, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), D-23845 Borstel, Germany
| | - Johannes Huebner
- Center for Infectious Disease and Travel Medicine, University Medical Center Freiburg, Freiburg, Germany Division of Pediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany
| |
Collapse
|
19
|
Luo Q, Li M, Fu H, Meng Q, Gao H. Shewanella oneidensis FabB: A β-ketoacyl-ACP Synthase That Works with C16:1-ACP. Front Microbiol 2016; 7:327. [PMID: 27014246 PMCID: PMC4793157 DOI: 10.3389/fmicb.2016.00327] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/01/2016] [Indexed: 12/12/2022] Open
Abstract
It is established that Escherichia coli β-ketoacyl-ACP synthase (KAS) I (encoded by EcfabB) is the primary, if not exclusive, factor for elongation of the cis-3-decenoyl-ACP (C10:1-ACP) but not effective with C16:1- or longer-chain-ACPs. To test the extent to which these features apply to KAS I proteins in other species, in this study, we examined the physiological role of FabB in Shewanella oneidensis, an excellent model for researching type II fatty acid synthetic (FAS) system and its regulation. We showed that the loss of either FabA (the enzyme that introduces double bond) or FabB, in the absence of DesA which desaturizes C16 and C18 to generate respective C16:1 and C18:1, leads to a UFA auxotroph. However, fatty acid profiles of membrane phospholipid of the fabA and fabB mutants are significantly different, suggesting that FabB participates in steps beyond elongation of C10:1-ACP. Further analyses demonstrated that S. oneidensis FabB differs from EcFabB in that (i) it is not the only enzyme capable of catalyzing elongation of the cis-3-decenoyl-ACP produced by FabA, (ii) it plays a critical role in elongation of C16:1- and longer-chain-ACPs, and (iii) its overproduction is detrimental.
Collapse
Affiliation(s)
- Qixia Luo
- Institute of Microbiology and College of Life Sciences, Zhejiang UniversityHangzhou, China; State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, College of Medicine, The First Affiliated Hospital, Zhejiang UniversityHangzhou, China
| | - Meng Li
- Institute of Microbiology and College of Life Sciences, Zhejiang University Hangzhou, China
| | - Huihui Fu
- Institute of Microbiology and College of Life Sciences, Zhejiang University Hangzhou, China
| | - Qiu Meng
- Institute of Microbiology and College of Life Sciences, Zhejiang University Hangzhou, China
| | - Haichun Gao
- Institute of Microbiology and College of Life Sciences, Zhejiang University Hangzhou, China
| |
Collapse
|
20
|
Zhou A, Hillesland KL, He Z, Schackwitz W, Tu Q, Zane GM, Ma Q, Qu Y, Stahl DA, Wall JD, Hazen TC, Fields MW, Arkin AP, Zhou J. Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris. ISME JOURNAL 2015; 9:2360-72. [PMID: 25848870 DOI: 10.1038/ismej.2015.45] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/07/2015] [Accepted: 02/26/2015] [Indexed: 01/19/2023]
Abstract
To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping data demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. Our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance.
Collapse
Affiliation(s)
- Aifen Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | | | - Zhili He
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Wendy Schackwitz
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Qichao Tu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Grant M Zane
- Departments of Biochemistry and Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO, USA
| | - Qiao Ma
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Yuanyuan Qu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - David A Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Judy D Wall
- Departments of Biochemistry and Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Matthew W Fields
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Adam P Arkin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| |
Collapse
|
21
|
Beld J, Lee DJ, Burkart MD. Fatty acid biosynthesis revisited: structure elucidation and metabolic engineering. MOLECULAR BIOSYSTEMS 2015; 11:38-59. [PMID: 25360565 PMCID: PMC4276719 DOI: 10.1039/c4mb00443d] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fatty acids are primary metabolites synthesized by complex, elegant, and essential biosynthetic machinery. Fatty acid synthases resemble an iterative assembly line, with an acyl carrier protein conveying the growing fatty acid to necessary enzymatic domains for modification. Each catalytic domain is a unique enzyme spanning a wide range of folds and structures. Although they harbor the same enzymatic activities, two different types of fatty acid synthase architectures are observed in nature. During recent years, strained petroleum supplies have driven interest in engineering organisms to either produce more fatty acids or specific high value products. Such efforts require a fundamental understanding of the enzymatic activities and regulation of fatty acid synthases. Despite more than one hundred years of research, we continue to learn new lessons about fatty acid synthases' many intricate structural and regulatory elements. In this review, we summarize each enzymatic domain and discuss efforts to engineer fatty acid synthases, providing some clues to important challenges and opportunities in the field.
Collapse
Affiliation(s)
- Joris Beld
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
| | | | | |
Collapse
|
22
|
The cold-induced two-component system CBO0366/CBO0365 regulates metabolic pathways with novel roles in group I Clostridium botulinum ATCC 3502 cold tolerance. Appl Environ Microbiol 2013; 80:306-19. [PMID: 24162575 DOI: 10.1128/aem.03173-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The two-component system CBO0366/CBO0365 was recently demonstrated to have a role in cold tolerance of group I Clostridium botulinum ATCC 3502. The mechanisms under its control, ultimately resulting in increased sensitivity to low temperature, are unknown. A transcriptomic analysis with DNA microarrays was performed to identify the differences in global gene expression patterns of the wild-type ATCC 3502 and a derivative mutant with insertionally inactivated cbo0365 at 37 and 15°C. Altogether, 150 or 141 chromosomal coding sequences (CDSs) were found to be differently expressed in the cbo0365 mutant at 37 or 15°C, respectively, and thus considered to be under the direct or indirect transcriptional control of the response regulator CBO0365. Of the differentially expressed CDSs, expression of 141 CDSs was similarly affected at both temperatures investigated, suggesting that the putative CBO0365 regulon was practically not affected by temperature. The regulon involved genes related to acetone-butanol-ethanol (ABE) fermentation, motility, arsenic resistance, and phosphate uptake and transport. Deteriorated growth at 17°C was observed for mutants with disrupted ABE fermentation pathway components (crt, bcd, bdh, and ctfA), arsenic detoxifying machinery components (arsC and arsR), or phosphate uptake mechanism components (phoT), suggesting roles for these mechanisms in cold tolerance of group I C. botulinum. Electrophoretic mobility shift assays showed recombinant CBO0365 to bind to the promoter regions of crt, arsR, and phoT, as well as to the promoter region of its own operon, suggesting direct DNA-binding transcriptional activation or repression as a means for CBO0365 in regulating these operons. The results provide insight to the mechanisms group I C. botulinum utilizes in coping with cold.
Collapse
|
23
|
FabQ, a dual-function dehydratase/isomerase, circumvents the last step of the classical fatty acid synthesis cycle. ACTA ACUST UNITED AC 2013; 20:1157-67. [PMID: 23972938 DOI: 10.1016/j.chembiol.2013.07.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 07/12/2013] [Accepted: 07/16/2013] [Indexed: 11/20/2022]
Abstract
In the classical anaerobic pathway of unsaturated fatty acid biosynthesis, that of Escherichia coli, the double bond is introduced into the growing acyl chain by the FabA dehydratase/isomerase. Another dehydratase, FabZ, functions in the chain elongation cycle. In contrast, Aerococcus viridans has only a single FabA/FabZ homolog we designate FabQ. FabQ can not only replace the function of E. coli FabZ in vivo, but it also catalyzes the isomerization required for unsaturated fatty acid biosynthesis. Most strikingly, FabQ in combination with E. coli FabB imparts the surprising ability to bypass reduction of the trans-2-acyl-ACP intermediates of classical fatty acid synthesis. FabQ allows elongation by progressive isomerization reactions to form the polyunsaturated fatty acid, 3-hydroxy-cis-5, 7-hexadecadienoic acid, both in vitro and in vivo. FabQ therefore provides a potential pathway for bacterial synthesis of polyunsaturated fatty acids.
Collapse
|
24
|
Parsons JB, Rock CO. Bacterial lipids: metabolism and membrane homeostasis. Prog Lipid Res 2013; 52:249-76. [PMID: 23500459 PMCID: PMC3665635 DOI: 10.1016/j.plipres.2013.02.002] [Citation(s) in RCA: 292] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/27/2013] [Accepted: 02/28/2013] [Indexed: 11/29/2022]
Abstract
Membrane lipid homeostasis is a vital facet of bacterial cell physiology. For decades, research in bacterial lipid synthesis was largely confined to the Escherichia coli model system. This basic research provided a blueprint for the biochemistry of lipid metabolism that has largely defined the individual steps in bacterial fatty acid and phospholipids synthesis. The advent of genomic sequencing has revealed a surprising amount of diversity in the genes, enzymes and genetic organization of the components responsible for bacterial lipid synthesis. Although the chemical steps in fatty acid synthesis are largely conserved in bacteria, there are surprising differences in the structure and cofactor requirements for the enzymes that perform these reactions in Gram-positive and Gram-negative bacteria. This review summarizes how the explosion of new information on the diversity of biochemical and genetic regulatory mechanisms has impacted our understanding of bacterial lipid homeostasis. The potential and problems of developing therapeutics that block pathogen phospholipid synthesis are explored and evaluated. The study of bacterial lipid metabolism continues to be a rich source for new biochemistry that underlies the variety and adaptability of bacterial life styles.
Collapse
Affiliation(s)
- Joshua B Parsons
- Department of Infectious Diseases, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | | |
Collapse
|
25
|
Adaptation in Haloalkaliphiles and Natronophilic Bacteria. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
26
|
LEI M, MA JC, WANG HH. Identification of Two Enoyl-ACP Reductase FabI1 and FabI2 in <I>Brucella abortus</I>*. PROG BIOCHEM BIOPHYS 2012. [DOI: 10.3724/sp.j.1206.2011.00463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
27
|
Schwarz KM, Kuit W, Grimmler C, Ehrenreich A, Kengen SWM. A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum--cellular behavior in adaptation to n-butanol. J Biotechnol 2012; 161:366-77. [PMID: 22484128 DOI: 10.1016/j.jbiotec.2012.03.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 03/05/2012] [Accepted: 03/21/2012] [Indexed: 12/18/2022]
Abstract
To gain more insight into the butanol stress response of Clostridium acetobutylicum the transcriptional response of a steady state acidogenic culture to different levels of n-butanol (0.25-1%) was investigated. No effect was observed on the fermentation pattern and expression of typical solvent genes (aad, ctfA/B, adc, bdhA/B, ptb, buk). Elevated levels of butanol mainly affected class I heat-shock genes (hrcA, grpE, dnaK, dnaJ, groES, groEL, hsp90), which were upregulated in a dose- and time-dependent manner, and genes encoding proteins involved in the membrane composition (fab and fad or glycerophospholipid related genes) and various ABC-transporters of unknown specificity. Interestingly, fab and fad genes were embedded in a large, entirely repressed cluster (CAC1988-CAC2019), which inter alia encoded an iron-specific ABC-transporter and molybdenum-cofactor synthesis proteins. Of the glycerophospholipid metabolism, the glycerol-3-phosphate dehydrogenase (glpA) gene was highly upregulated, whereas a glycerophosphodiester ABC-transporter (ugpAEBC) and a phosphodiesterase (ugpC) were repressed. On the megaplasmid, only a few genes showed differential expression, e.g. a rare lipoprotein (CAP0058, repressed) and a membrane protein (CAP0102, upregulated) gene. Observed transcriptional responses suggest that C. acetobutylicum reacts to butanol stress by induction of the general stress response and changing its cell envelope and transporter composition, but leaving the central catabolism unaffected.
Collapse
Affiliation(s)
- Katrin M Schwarz
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | | | | | | | | |
Collapse
|
28
|
de Sarrau B, Clavel T, Clerté C, Carlin F, Giniès C, Nguyen-The C. Influence of anaerobiosis and low temperature on Bacillus cereus growth, metabolism, and membrane properties. Appl Environ Microbiol 2012; 78:1715-23. [PMID: 22247126 PMCID: PMC3298147 DOI: 10.1128/aem.06410-11] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 01/02/2012] [Indexed: 02/02/2023] Open
Abstract
The impact of simultaneous anaerobiosis and low temperature on growth parameters, metabolism, and membrane properties of Bacillus cereus ATCC 14579 was studied. No growth was observed under anaerobiosis at 12°C. In bioreactors, growth rates and biomass production were drastically reduced by simultaneous anaerobiosis and low temperature (15°C). The two conditions had a synergistic effect on biomass reduction. In anaerobic cultures, fermentative metabolism was modified by low temperature, with a marked reduction in ethanol production leading to a lower ability to produce NAD(+). Anaerobiosis reduced unsaturated fatty acids at both low optimal temperatures. In addition, simultaneous anaerobiosis and low temperatures markedly reduced levels of branched-chain fatty acids compared to all other conditions (accounting for 33% of total fatty acids against more 71% for low-temperature aerobiosis, optimal-temperature aerobiosis, and optimal-temperature anaerobiosis). This corresponded to high-melting-temperature lipids and to low-fluidity membranes, as indicated by differential scanning calorimetry, 1,6-diphenyl-1,3,5-hexatriene (DPH) fluorescence anisotropy, and infrared spectroscopy. This is in contrast to requirements for cold adaptation. A link between modification in the synthesis of metabolites of fermentative metabolism and the reduction of branched-chain fatty acids at low temperature under anaerobiosis, through a modification of the oxidizing capacity, is assumed. This link may partly explain the impact of low temperature and anaerobiosis on membrane properties and growth performance.
Collapse
Affiliation(s)
- Benoît de Sarrau
- INRA, UMR408 Sécurité et Qualité des Produits d’Origine Végétale, Avignon, France.
| | | | | | | | | | | |
Collapse
|
29
|
Bi H, Christensen QH, Feng Y, Wang H, Cronan JE. The Burkholderia cenocepacia BDSF quorum sensing fatty acid is synthesized by a bifunctional crotonase homologue having both dehydratase and thioesterase activities. Mol Microbiol 2012; 83:840-55. [PMID: 22221091 DOI: 10.1111/j.1365-2958.2012.07968.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Signal molecules of the diffusible signal factor (DSF) family have been shown recently to be involved in regulation of pathogenesis and biofilm formation in diverse Gram-negative bacteria. DSF signals are reported to be active not only on their cognate bacteria, but also on unrelated bacteria and the pathogenic yeast, Candida albicans. DSFs are monounsaturated fatty acids of medium chain length containing an unusual cis-2 double bond. Although genetic analyses had identified genes involved in DSF synthesis, the pathway of DSF synthesis was unknown. The DSF of the important human pathogen Burkholderia cenocepacia (called BDSF) is cis-2-dodecenoic acid. We report that BDSF is synthesized from a fatty acid synthetic intermediate, the acyl carrier protein (ACP) thioester of 3-hydroxydodecanoic acid. This intermediate is intercepted by protein Bcam0581 and converted to cis-2-dodecenoyl-ACP. Bcam0581 is annotated as a homologue of crotonase, the first enzyme of the fatty acid degradation pathway. We demonstrated Bcam0581to be a bifunctional protein that not only catalysed dehydration of 3-hydroxydodecanoyl-ACP to cis-2-dodecenoyl-ACP, but also cleaved the thioester bond to give the free acid. Both activities required the same set of active-site residues. Although dehydratase and thioesterase activities are known activities of the crotonase superfamily, Bcam0581 is the first protein shown to have both activities.
Collapse
Affiliation(s)
- Hongkai Bi
- Departments of Microbiology Biochemistry, B103 Chemical and Life Sciences Laboratory, University of Illinois, 601 S. Goodwin Ave, Urbana, IL 61801, USA
| | | | | | | | | |
Collapse
|
30
|
Only one of the five Ralstonia solanacearum long-chain 3-ketoacyl-acyl carrier protein synthase homologues functions in fatty acid synthesis. Appl Environ Microbiol 2011; 78:1563-73. [PMID: 22194290 DOI: 10.1128/aem.07335-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ralstonia solanacearum, a major phytopathogenic bacterium, causes a bacterial wilt disease in diverse plants. Although fatty acid analyses of total membranes of R. solanacearum showed that they contain primarily palmitic (C(16:0)), palmitoleic (C(16:1)) and cis-vaccenic (C(18:1)) acids, little is known regarding R. solanacearum fatty acid synthesis. The R. solanacearum GMI1000 genome is unusual in that it contains four genes (fabF1, fabF2, fabF3, and fabF4) annotated as encoding 3-ketoacyl-acyl carrier protein synthase II homologues and one gene (fabB) annotated as encoding 3-ketoacyl-acyl carrier protein synthase I. We have analyzed this puzzling apparent redundancy and found that only one of these genes, fabF1, encoded a long-chain 3-ketoacyl-acyl carrier protein synthase, whereas the other homologues did not play roles in R. solanacearum fatty acid synthesis. Mutant strains lacking fabF1 are nonviable, and thus, FabF1 is essential for R. solanacearum fatty acid biosynthesis. Moreover, R. solanacearum FabF1 has the activities of both 3-ketoacyl-acyl carrier protein synthase II and 3-ketoacyl-acyl carrier protein synthase I.
Collapse
|
31
|
Isabella VM, Clark VL. Identification of a conserved protein involved in anaerobic unsaturated fatty acid synthesis in Neiserria gonorrhoeae: implications for facultative and obligate anaerobes that lack FabA. Mol Microbiol 2011; 82:489-501. [PMID: 21895795 DOI: 10.1111/j.1365-2958.2011.07826.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Transcriptome analysis of the facultative anaerobe, Neisseria gonorrhoeae, revealed that many genes of unknown function were induced under anaerobic conditions. Mutation of one such gene, NGO1024, encoding a protein belonging to the 2-nitropropane dioxygenase-like superfamily of proteins, was found to result in an inability of gonococci to grow anaerobically. Anaerobic growth of an NG1024 mutant was restored upon supplementation with unsaturated fatty acids (UFA), but not with the saturated fatty acid palmitate. Gonococcal fatty acid profiles confirmed that NGO1024 was involved in UFA synthesis anaerobically, but not aerobically, demonstrating that gonococci contain two distinct pathways for the production of UFAs, with a yet unidentified aerobic mechanism, and an anaerobic mechanism involving NGO1024. Expression of genes involved in classical anaerobic UFA synthesis, fabA, fabM and fabB, was toxic in gonococci and unable to complement a NGO1024 mutation, suggesting that the chemistry involved in gonococcal anaerobic UFA synthesis is distinct from that of the classical pathway. NGO1024 homologues, which we suggest naming UfaA, form a distinct lineage within the 2-nitropropane dioxygenase-like superfamily, and are found in many facultative and obligate anaerobes that produce UFAs but lack fabA, suggesting that UfaA is part of a widespread pathway involved in UFA synthesis.
Collapse
Affiliation(s)
- Vincent M Isabella
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Box 672, 601 Elmwood Ave, Rochester, NY 14642, USA
| | | |
Collapse
|
32
|
Curreem SO, Teng JL, Tse H, Yuen KY, Lau SK, Woo PC. General metabolism of Laribacter hongkongensis: a genome-wide analysis. Cell Biosci 2011; 1:16. [PMID: 21711917 PMCID: PMC3125206 DOI: 10.1186/2045-3701-1-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 04/19/2011] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler's diarrhea. In this study, we performed an in-depth annotation of the genes and pathways of the general metabolism of L. hongkongensis and correlated them with its phenotypic characteristics. RESULTS The L. hongkongensis genome possesses the pentose phosphate and gluconeogenesis pathways and tricarboxylic acid and glyoxylate cycles, but incomplete Embden-Meyerhof-Parnas and Entner-Doudoroff pathways, in agreement with its asaccharolytic phenotype. It contains enzymes for biosynthesis and β-oxidation of saturated fatty acids, biosynthesis of all 20 universal amino acids and selenocysteine, the latter not observed in Neisseria gonorrhoeae, Neisseria meningitidis and Chromobacterium violaceum. The genome contains a variety of dehydrogenases, enabling it to utilize different substrates as electron donors. It encodes three terminal cytochrome oxidases for respiration using oxygen as the electron acceptor under aerobic and microaerophilic conditions and four reductases for respiration with alternative electron acceptors under anaerobic conditions. The presence of complete tetrathionate reductase operon may confer survival advantage in mammalian host in association with diarrhea. The genome contains CDSs for incorporating sulfur and nitrogen by sulfate assimilation, ammonia assimilation and nitrate reduction. The existence of both glutamate dehydrogenase and glutamine synthetase/glutamate synthase pathways suggests an importance of ammonia metabolism in the living environments that it may encounter. CONCLUSIONS The L. hongkongensis genome possesses a variety of genes and pathways for carbohydrate, amino acid and lipid metabolism, respiratory chain and sulfur and nitrogen metabolism. These allow the bacterium to utilize various substrates for energy production and survive in different environmental niches.
Collapse
Affiliation(s)
- Shirly O Curreem
- Department of Microbiology, The University of Hong Kong, Hong Kong.
| | | | | | | | | | | |
Collapse
|
33
|
Mao S, Luo Y, Bao G, Zhang Y, Li Y, Ma Y. Comparative analysis on the membrane proteome of Clostridium acetobutylicum wild type strain and its butanol-tolerant mutant. MOLECULAR BIOSYSTEMS 2011; 7:1660-77. [DOI: 10.1039/c0mb00330a] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
34
|
Abstract
FA (fatty acid) synthesis represents a central, conserved process by which acyl chains are produced for utilization in a number of end-products such as biological membranes. Central to FA synthesis, the ACP (acyl carrier protein) represents the cofactor protein that covalently binds all fatty acyl intermediates via a phosphopantetheine linker during the synthesis process. FASs (FA synthases) can be divided into two classes, type I and II, which are primarily present in eukaryotes and bacteria/plants respectively. They are characterized by being composed of either large multifunctional polypeptides in the case of type I or consisting of discretely expressed mono-functional proteins in the type II system. Owing to this difference in architecture, the FAS system has been thought to be a good target for the discovery of novel antibacterial agents, as exemplified by the antituberculosis drug isoniazid. There have been considerable advances in this field in recent years, including the first high-resolution structural insights into the type I mega-synthases and their dynamic behaviour. Furthermore, the structural and dynamic properties of an increasing number of acyl-ACPs have been described, leading to an improved comprehension of this central carrier protein. In the present review we discuss the state of the understanding of FA synthesis with a focus on ACP. In particular, developments made over the past few years are highlighted.
Collapse
|
35
|
Increasing unsaturated fatty acid contents in Escherichia coli by coexpression of three different genes. Appl Microbiol Biotechnol 2010; 87:271-80. [DOI: 10.1007/s00253-009-2377-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 11/19/2009] [Accepted: 11/20/2009] [Indexed: 11/26/2022]
|