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Hernández MA, Ledesma AE, Moncalián G, Alvarez HM. MLDSR, the transcriptional regulator of the major lipid droplets protein MLDS, is controlled by long-chain fatty acids and contributes to the lipid-accumulating phenotype in oleaginous Rhodococcus strains. FEBS J 2024; 291:1457-1482. [PMID: 38135896 DOI: 10.1111/febs.17043] [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: 08/31/2023] [Revised: 11/08/2023] [Accepted: 12/21/2023] [Indexed: 12/24/2023]
Abstract
Microorganism lipid droplet small regulator (MLDSR) is a transcriptional regulator of the major lipid droplet (LD)-associated protein MLDS in Rhodococcus jostii RHA1 and Rhodococcus opacus PD630. In this study, we investigated the role of MLDSR on lipid metabolism and triacylglycerol (TAG) accumulation in R. jostii RHA1 at physiological and molecular levels. MLDSR gene deletion promoted a significant decrease of TAG accumulation, whereas inhibition of de novo fatty acid biosynthesis by the addition of cerulenin significantly repressed the expression of the mldsr-mlds cluster under nitrogen-limiting conditions. In vitro and in vivo approaches revealed that MLDSR-DNA binding is inhibited by fatty acids and acyl-CoA residues through changes in the oligomeric or conformational state of the protein. RNAseq analysis indicated that MLDSR not only controls the expression of its own gene cluster but also of several genes involved in central, lipid, and redox metabolism, among others. We also identified putative MLDSR-binding sites on the upstream regions of genes coding for lipid catabolic enzymes and validated them by EMSA assays. Overexpression of mldsr gene under nitrogen-rich conditions promoted an increase of TAG accumulation, and further cell lysis with TAG release to the culture medium. Our results suggested that MLDSR is a fatty acid-responsive regulator that plays a dual role in cells by repression or activation of several metabolic genes in R. jostii RHA1. MLDSR seems to play an important role in the fine-tuning regulation of TAG accumulation, LD formation, and cellular lipid homeostasis, contributing to the oleaginous phenotype of R. jostii RHA1 and R. opacus PD630.
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Affiliation(s)
- Martín A Hernández
- INBIOP (Instituto de Biociencias de la Patagonia), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco, Comodoro Rivadavia, Argentina
| | - Ana E Ledesma
- CIBAAL (Centro de Investigación en Biofísica Aplicada y Alimentos), Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Santiago del Estero, Argentina
| | - Gabriel Moncalián
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, Santander, Spain
| | - Héctor M Alvarez
- INBIOP (Instituto de Biociencias de la Patagonia), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco, Comodoro Rivadavia, Argentina
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2
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Li X, Gluth A, Feng S, Qian WJ, Yang B. Harnessing redox proteomics to study metabolic regulation and stress response in lignin-fed Rhodococci. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:180. [PMID: 37986172 PMCID: PMC10662689 DOI: 10.1186/s13068-023-02424-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 11/02/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Rhodococci are studied for their bacterial ligninolytic capabilities and proclivity to accumulate lipids. Lignin utilization is a resource intensive process requiring a variety of redox active enzymes and cofactors for degradation as well as defense against the resulting toxic byproducts and oxidative conditions. Studying enzyme expression and regulation between carbon sources will help decode the metabolic rewiring that stymies lignin to lipid conversion in these bacteria. Herein, a redox proteomics approach was applied to investigate a fundamental driver of carbon catabolism and lipid anabolism: redox balance. RESULTS A consortium of Rhodococcus strains was employed in this study given its higher capacity for lignin degradation compared to monocultures. This consortium was grown on glucose vs. lignin under nitrogen limitation to study the importance of redox balance as it relates to nutrient availability. A modified bottom-up proteomics workflow was harnessed to acquire a general relationship between protein abundance and protein redox states. Global proteomics results affirm differential expression of enzymes involved in sugar metabolism vs. those involved in lignin degradation and aromatics metabolism. As reported previously, several enzymes in the lipid biosynthetic pathways were downregulated, whereas many involved in β-oxidation were upregulated. Interestingly, proteins involved in oxidative stress response were also upregulated perhaps in response to lignin degradation and aromatics catabolism, which require oxygen and reactive oxygen species and generate toxic byproducts. Enzymes displaying little-to-no change in abundance but differences in redox state were observed in various pathways for carbon utilization (e.g., β‑ketoadipate pathway), lipid metabolism, as well as nitrogen metabolism (e.g., purine scavenging/synthesis), suggesting potential mechanisms of redox-dependent regulation of metabolism. CONCLUSIONS Efficient lipid production requires a steady carbon and energy flux while balancing fundamental requirements for enzyme production and cell maintenance. For lignin, we theorize that this balance is difficult to establish due to resource expenditure for enzyme production and stress response. This is supported by significant changes to protein abundances and protein cysteine oxidation in various metabolic pathways and redox processes.
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Affiliation(s)
- Xiaolu Li
- Bioproducts, Sciences, and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, WA, 99354, USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Austin Gluth
- Bioproducts, Sciences, and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, WA, 99354, USA
| | - Song Feng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Bin Yang
- Bioproducts, Sciences, and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, WA, 99354, USA.
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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3
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Engelhart-Straub S, Cavelius P, Hölzl F, Haack M, Awad D, Brueck T, Mehlmer N. Effects of Light on Growth and Metabolism of Rhodococcus erythropolis. Microorganisms 2022; 10:microorganisms10081680. [PMID: 36014097 PMCID: PMC9416670 DOI: 10.3390/microorganisms10081680] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
Rhodococcus erythropolis is resilient to various stressors. However, the response of R. erythropolis towards light has not been evaluated. In this study, R. erythropolis was exposed to different wavelengths of light. Compared to non-illuminated controls, carotenoid levels were significantly increased in white (standard warm white), green (510 nm) and blue light (470 nm) illuminated cultures. Notably, blue light (455, 425 nm) exhibited anti-microbial effects. Interestingly, cellular lipid composition shifted under light stress, increasing odd chain fatty acids (C15:0, C17:1) cultured under white (standard warm white) and green (510 nm) light. When exposed to blue light (470, 455, 425 nm), fatty acid profiles shifted to more saturated fatty acids (C16:1 to C16:0). Time-resolved proteomics analysis revealed several oxidative stress-related proteins to be upregulated under light illumination.
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Alvarez HM, Hernández MA, Lanfranconi MP, Silva RA, Villalba MS. Rhodococcus as Biofactories for Microbial Oil Production. Molecules 2021; 26:molecules26164871. [PMID: 34443455 PMCID: PMC8401914 DOI: 10.3390/molecules26164871] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/20/2023] Open
Abstract
Bacteria belonging to the Rhodococcus genus are frequent components of microbial communities in diverse natural environments. Some rhodococcal species exhibit the outstanding ability to produce significant amounts of triacylglycerols (TAG) (>20% of cellular dry weight) in the presence of an excess of the carbon source and limitation of the nitrogen source. For this reason, they can be considered as oleaginous microorganisms. As occurs as well in eukaryotic single-cell oil (SCO) producers, these bacteria possess specific physiological properties and molecular mechanisms that differentiate them from other microorganisms unable to synthesize TAG. In this review, we summarized several of the well-characterized molecular mechanisms that enable oleaginous rhodococci to produce significant amounts of SCO. Furthermore, we highlighted the ability of these microorganisms to degrade a wide range of carbon sources coupled to lipogenesis. The qualitative and quantitative oil production by rhodococci from diverse industrial wastes has also been included. Finally, we summarized the genetic and metabolic approaches applied to oleaginous rhodococci to improve SCO production. This review provides a comprehensive and integrating vision on the potential of oleaginous rhodococci to be considered as microbial biofactories for microbial oil production.
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5
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Mallick I, Santucci P, Poncin I, Point V, Kremer L, Cavalier JF, Canaan S. Intrabacterial lipid inclusions in mycobacteria: unexpected key players in survival and pathogenesis? FEMS Microbiol Rev 2021; 45:6283747. [PMID: 34036305 DOI: 10.1093/femsre/fuab029] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 05/21/2021] [Indexed: 12/12/2022] Open
Abstract
Mycobacterial species, including Mycobacterium tuberculosis, rely on lipids to survive and chronically persist within their hosts. Upon infection, opportunistic and strict pathogenic mycobacteria exploit metabolic pathways to import and process host-derived free fatty acids, subsequently stored as triacylglycerols under the form of intrabacterial lipid inclusions (ILI). Under nutrient-limiting conditions, ILI constitute a critical source of energy that fuels the carbon requirements and maintain redox homeostasis, promoting bacterial survival for extensive periods of time. In addition to their basic metabolic functions, these organelles display multiple other biological properties, emphasizing their central role in the mycobacterial lifecycle. However, despite of their importance, the dynamics of ILI metabolism and their contribution to mycobacterial adaptation/survival in the context of infection has not been thoroughly documented. Herein, we provide an overview of the historical ILI discoveries, their characterization, and current knowledge regarding the micro-environmental stimuli conveying ILI formation, storage and degradation. We also review new biological systems to monitor the dynamics of ILI metabolism in extra- and intracellular mycobacteria and describe major molecular actors in triacylglycerol biosynthesis, maintenance and breakdown. Finally, emerging concepts regarding to the role of ILI in mycobacterial survival, persistence, reactivation, antibiotic susceptibility and inter-individual transmission are also discuss.
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Affiliation(s)
- Ivy Mallick
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille Univ., Marseille, France
| | - Pierre Santucci
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Isabelle Poncin
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Vanessa Point
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, Montpellier, France.,IRIM, INSERM, Montpellier, France
| | | | - Stéphane Canaan
- Aix-Marseille Univ, CNRS, LISM, IMM FR3479, Marseille, France
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6
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Sineli PE, Herrera HM, Aparicio JD, Guerrero DS, Polti MA, Dávila Costa JS. Genomic analysis and proteomic response of the chromium-resistant and phenanthrene-degrading strain Streptomyces sp. MC1. J Appl Microbiol 2021; 131:719-727. [PMID: 33434397 DOI: 10.1111/jam.15002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/26/2020] [Accepted: 01/08/2021] [Indexed: 11/28/2022]
Abstract
AIM Chemically disparate toxic organic and/or inorganic molecules produced by anthropogenic activities often hinder the bioremediation process. This research was conducted to understand the capacity of Streptomyces sp. MC1 to remove chemically disparate toxics such as Cr(VI) or phenanthrene. METHODS AND RESULTS Genomic, metabolic modeling and proteomic approaches were used in this study. Our results demonstrated that Streptomyces sp. MC1 has the genetic determinants to remove Cr(VI) or degrade phenanthrene. Proteomics showed that these genetic determinants were expressed. Metabolic versatility of the strain was confirmed by two metabolic models in complex and minimal media. Interestingly, our results also suggested a connection between the degradation of phenanthrene and synthesis of specialized metabolites. CONCLUSIONS Streptomyces sp. MC1 has the genetic and physiological potential to remove Cr(VI) or degrade phenanthrene SIGNIFICANCE AND IMPACT OF STUDY: The probability of a microorganism to survive in the presence of different contaminants depends on its genetic potential and the ability to express it. The genetic and proteomic profiles obtained for Streptomyces sp. MC1 can be recommended as model and predict if other Streptomyces strains can be used in bioremediation processes. Our work also hypothesized that intermediates of the phenanthrene degradation serve as precursors for the specialized metabolism.
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Affiliation(s)
- P E Sineli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina
| | - H M Herrera
- Universidad Nacional de Tucumán, Argentina, Tucumán, Argentina
| | - J D Aparicio
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina.,Universidad Nacional de Tucumán, Argentina, Tucumán, Argentina
| | - D S Guerrero
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina
| | - M A Polti
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina.,Universidad Nacional de Tucumán, Argentina, Tucumán, Argentina
| | - J S Dávila Costa
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), San Miguel de Tucumán, Argentina
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7
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Hwangbo M, Gill JJ, Young R, Chu KH. Dual-function oleaginous biocatalysts for non-sterile cultivation and solvent-free biolipid bioextraction to reduce biolipid-based biofuel production costs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 758:143969. [PMID: 33333303 PMCID: PMC8061307 DOI: 10.1016/j.scitotenv.2020.143969] [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: 09/06/2020] [Revised: 10/31/2020] [Accepted: 11/14/2020] [Indexed: 06/12/2023]
Abstract
Triacylglycerols (TAGs) are starting materials for the production of biolipid-based fuels such as biodiesel and biojet fuel. While various microorganisms can produce TAGs from renewable resources, the cultivation of TAG-producing microorganisms under sterilization conditions to avoid microbial contamination and application of solvent to extract TAGs from the TAG-filled microorganisms are costly. To overcome these challenges, this study reports the feasibility of a non-sterile cultivation of an oleaginous bacterium Rhodococcus opacus PD631SpAHB under saline conditions, followed by the use of a solvent-free, phage-lysis-protein-based bioextraction approach for TAGs release. The engineered strain PD631SpAHB was developed by introducing a recombinant plasmid carrying a phage lytic gene cassette (pAHB) into Rhodococcus opacus PD631 via transformation, followed by adaptive evolution under saline conditions. This newly developed strain is a salt-tolerant strain with the inducible plasmid pAHB to enable TAGs release into the supernatant upon induction. Cell lysis of PD631SpAHB was confirmed by the decrease of the optical density of cell suspension, by the loss of cell membrane integrity, and by the detection of TAGs in the culture medium. Up to 38% of the total TAGs accumulated in PD631SpAHB was released into supernatant after the expression of the lytic genes. PD631SpAHB strain is a promising candidate to produce TAGs from non-sterile growth medium and release of its TAGs without solvent extraction - a new approach to reduce the overall cost of biolipid-based biofuel production.
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Affiliation(s)
- Myung Hwangbo
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Jason J Gill
- Department of Animal Science, Texas A&M University, College Station, TX 77843, United States; Center for Phage Technology, Texas A&M University, College Station, TX 77843, United States
| | - Ry Young
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, United States; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX 77843, United States.
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8
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Pátek M, Grulich M, Nešvera J. Stress response in Rhodococcus strains. Biotechnol Adv 2021; 53:107698. [PMID: 33515672 DOI: 10.1016/j.biotechadv.2021.107698] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 12/13/2022]
Abstract
Rhodococci are bacteria which can survive under various extreme conditions, in the presence of toxic compounds, and in other hostile habitats. Their tolerance of unfavorable conditions is associated with the structure of their cell wall and their large array of enzymes, which degrade or detoxify harmful compounds. Their physiological and biotechnological properties, together with tools for their genetic manipulation, enable us to apply them in biotransformations, biodegradation and bioremediation. Many such biotechnological applications cause stresses that positively or negatively affect their efficiency. Whereas numerous reviews on rhodococci described their enzyme activities, the optimization of degradation or production processes, and corresponding technological solutions, only a few reviews discussed some specific effects of stresses on the physiology of rhodococci and biotechnological processes. This review aims to comprehensively describe individual stress responses in Rhodococcus strains, the interconnection of different types of stresses and their consequences for cell physiology. We examine here the responses to (1) environmental stresses (desiccation, heat, cold, osmotic and pH stress), (2) the presence of stress-inducing compounds (metals, organic compounds and antibiotics) in the environment (3) starvation and (4) stresses encountered during biotechnological applications. Adaptations of the cell envelope, the formation of multicellular structures and stresses induced by the interactions of hosts with pathogenic rhodococci are also included. The roles of sigma factors of RNA polymerase in the global regulation of stress responses in rhodococci are described as well. Although the review covers a large number of stressful conditions, our intention was to provide an overview of the selected stress responses and their possible connection to biotechnological processes, not an exhaustive survey of the scientific literature. The findings on stress responses summarized in this review and the demonstration of gaps in current knowledge may motivate researchers working to fill these gaps.
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Affiliation(s)
- Miroslav Pátek
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
| | - Michal Grulich
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
| | - Jan Nešvera
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
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9
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Xu Z, Pan C, Li X, Hao N, Zhang T, Gaffrey MJ, Pu Y, Cort JR, Ragauskas AJ, Qian WJ, Yang B. Enhancement of polyhydroxyalkanoate production by co-feeding lignin derivatives with glycerol in Pseudomonas putida KT2440. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:11. [PMID: 33413621 PMCID: PMC7792162 DOI: 10.1186/s13068-020-01861-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Efficient utilization of all available carbons from lignocellulosic biomass is critical for economic efficiency of a bioconversion process to produce renewable bioproducts. However, the metabolic responses that enable Pseudomonas putida to utilize mixed carbon sources to generate reducing power and polyhydroxyalkanoate (PHA) remain unclear. Previous research has mainly focused on different fermentation strategies, including the sequential feeding of xylose as the growth stage substrate and octanoic acid as the PHA-producing substrate, feeding glycerol as the sole carbon substrate, and co-feeding of lignin and glucose. This study developed a new strategy-co-feeding glycerol and lignin derivatives such as benzoate, vanillin, and vanillic acid in Pseudomonas putida KT2440-for the first time, which simultaneously improved both cell biomass and PHA production. RESULTS Co-feeding lignin derivatives (i.e. benzoate, vanillin, and vanillic acid) and glycerol to P. putida KT2440 was shown for the first time to simultaneously increase cell dry weight (CDW) by 9.4-16.1% and PHA content by 29.0-63.2%, respectively, compared with feeding glycerol alone. GC-MS results revealed that the addition of lignin derivatives to glycerol decreased the distribution of long-chain monomers (C10 and C12) by 0.4-4.4% and increased the distribution of short-chain monomers (C6 and C8) by 0.8-3.5%. The 1H-13C HMBC, 1H-13C HSQC, and 1H-1H COSY NMR analysis confirmed that the PHA monomers (C6-C14) were produced when glycerol was fed to the bacteria alone or together with lignin derivatives. Moreover, investigation of the glycerol/benzoate/nitrogen ratios showed that benzoate acted as an independent factor in PHA synthesis. Furthermore, 1H, 13C and 31P NMR metabolite analysis and mass spectrometry-based quantitative proteomics measurements suggested that the addition of benzoate stimulated oxidative-stress responses, enhanced glycerol consumption, and altered the intracellular NAD+/NADH and NADPH/NADP+ ratios by up-regulating the proteins involved in energy generation and storage processes, including the Entner-Doudoroff (ED) pathway, the reductive TCA route, trehalose degradation, fatty acid β-oxidation, and PHA biosynthesis. CONCLUSIONS This work demonstrated an effective co-carbon feeding strategy to improve PHA content/yield and convert lignin derivatives into value-added products in P. putida KT2440. Co-feeding lignin break-down products with other carbon sources, such as glycerol, has been demonstrated as an efficient way to utilize biomass to increase PHA production in P. putida KT2440. Moreover, the involvement of aromatic degradation favours further lignin utilization, and the combination of proteomics and metabolomics with NMR sheds light on the metabolic and regulatory mechanisms for cellular redox balance and potential genetic targets for a higher biomass carbon conversion efficiency.
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Affiliation(s)
- Zhangyang Xu
- Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, WA, 99354, USA
| | - Chunmei Pan
- Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, WA, 99354, USA
- College of Food and Bioengineering, Henan University of Animal Husbandry and Economy, Zhengzhou, 450046, Henan, China
| | - Xiaolu Li
- Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, WA, 99354, USA
| | - Naijia Hao
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, 37996, USA
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Matthew J Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yunqiao Pu
- Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - John R Cort
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Arthur J Ragauskas
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, 37996, USA
- Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Bin Yang
- Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, WA, 99354, USA.
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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10
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Differential protein profiling of soil diazotroph Rhodococcus qingshengii S10107 towards low-temperature and nitrogen deficiency. Sci Rep 2019; 9:20378. [PMID: 31889061 PMCID: PMC6937269 DOI: 10.1038/s41598-019-56592-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/03/2019] [Indexed: 01/01/2023] Open
Abstract
Protein-based biomarkers can be a promising approach for identification and real-time monitoring of the bio-inoculants employed under sustainable agricultural plans. In this perspective, differential proteomics of psychrophilic diazotroph Rhodococcus qingshengii S10107 (JX173283) was performed to unravel its adaptive responses towards low-temperature nitrogen deficiency and identification of a biomarker for respective physiological conditions. LC-MS/MS-based proteome analysis mapped more than 4830 proteins including 77 up-regulated and 47 down-regulated proteins (p ≤ 0.05). Differential expression of the structural genes of nif regulon viz. nifH, nifD, and nifK along with their response regulators i.e. nifA, nifL, and nifB indicated that the nitrogenase complex was activated successfully. Besides up-regulating the biosynthesis of certain amino acids viz. Leucine, Lysine, and Alanine; the expression of the peptidoglycan synthesis proteins were also increased; while, the enzymes involved in Lipid biosynthesis were found to decrease. Furthermore, two important enzymes of the pentose phosphate pathway viz. Transketolase and Transaldolase along with Ribose import ATP-binding protein RbsA were also found to induce significantly under low temperature a nitrogen deficient condition, which suggests the cellular need for ample ribose sugar instantly. Additionally, comparative protein profiling of S10107 strain with our previous studies revealed that CowN protein was significantly up-regulated in all the cases under low-temperature nitrogen deficient conditions and therefore, can be developed as a biomarker. Conclusively, present study for the first time provides an in-depth proteome profiling of R. qingshengii S10107 and proclaims CowN as a potential protein biomarker for monitoring BNF under cold niches.
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11
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Bonilla JO, Callegari EA, Estevéz MC, Villegas LB. Intracellular Proteomic Analysis of Streptomyces sp. MC1 When Exposed to Cr(VI) by Gel-Based and Gel-Free Methods. Curr Microbiol 2019; 77:62-70. [PMID: 31705393 DOI: 10.1007/s00284-019-01790-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023]
Abstract
The actinobacterium Streptomyces sp. MC1 has previously shown the capacity to resist and remove Cr(VI) from liquid culture media. The aim of this work is to analyze the differential expression pattern of intracellular proteins when Streptomyces sp. MC1 is exposed to Cr(VI) in order to explain the molecular mechanisms of resistance that this microorganism possesses. For this purpose, 2D-PAGE and shotgun proteomic analyses (2D-nanoUPLC-ESI-MS/MS) were applied. The presence of Cr(VI) induced the expression of proteins involved in molecular biosynthesis and energy generation, chaperones with a key role in the repair of misfolded proteins and stress response, transcription proteins, proteins of importance in the DNA supercoiling, repair and replication, and dehydrogenases involved in oxidation-reduction processes. These dehydrogenases can be associated with the reduction of Cr(VI) to Cr(III). The results of this study show that proteins from the groups mentioned before are important to face the stress caused by the Cr(VI) presence and help the microorganism to counteract the toxicity of the metal. The use of two proteomic approaches resulted in a larger number of peptides identified, which is also transduced in a significant number of protein ID. This decreased the potential complexity of the sample because of the protein dynamic range, as well as increased the recovery of peptides from the gel after digestion.
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Affiliation(s)
- José O Bonilla
- Instituto de Química San Luis (INQUISAL), CONICET, Chacabuco 917, 5700, San Luis, Argentina.,Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700, San Luis, Argentina
| | - Eduardo A Callegari
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - María C Estevéz
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CONICET, Av. Belgrano y Pje. Caseros, 4000, Tucumán, Argentina.,Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, 4000, Tucumán, Argentina
| | - Liliana B Villegas
- Instituto de Química San Luis (INQUISAL), CONICET, Chacabuco 917, 5700, San Luis, Argentina. .,Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700, San Luis, Argentina.
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Li X, He Y, Zhang L, Xu Z, Ben H, Gaffrey MJ, Yang Y, Yang S, Yuan JS, Qian WJ, Yang B. Discovery of potential pathways for biological conversion of poplar wood into lipids by co-fermentation of Rhodococci strains. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:60. [PMID: 30923568 PMCID: PMC6423811 DOI: 10.1186/s13068-019-1395-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/06/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Biological routes for utilizing both carbohydrates and lignin are important to reach the ultimate goal of bioconversion of full carbon in biomass into biofuels and biochemicals. Recent biotechnology advances have shown promises toward facilitating biological transformation of lignin into lipids. Natural and engineered Rhodococcus strains (e.g., R. opacus PD630, R. jostii RHA1, and R. jostii RHA1 VanA-) have been demonstrated to utilize lignin for lipid production, and co-culture of them can promote lipid production from lignin. RESULTS In this study, a co-fermentation module of natural and engineered Rhodococcus strains with significant improved lignin degradation and/or lipid biosynthesis capacities was established, which enabled simultaneous conversion of glucose, lignin, and its derivatives into lipids. Although Rhodococci sp. showed preference to glucose over lignin, nearly half of the lignin was quickly depolymerized to monomers by these strains for cell growth and lipid synthesis after glucose was nearly consumed up. Profiles of metabolites produced by Rhodococcus strains growing on different carbon sources (e.g., glucose, alkali lignin, and dilute acid flowthrough-pretreated poplar wood slurry) confirmed lignin conversion during co-fermentation, and indicated novel metabolic capacities and unexplored metabolic pathways in these organisms. Proteome profiles suggested that lignin depolymerization by Rhodococci sp. involved multiple peroxidases with accessory oxidases. Besides the β-ketoadipate pathway, the phenylacetic acid (PAA) pathway was another potential route for the in vivo ring cleavage activity. In addition, deficiency of reducing power and cellular oxidative stress probably led to lower lipid production using lignin as the sole carbon source than that using glucose. CONCLUSIONS This work demonstrated a potential strategy for efficient bioconversion of both lignin and glucose into lipids by co-culture of multiple natural and engineered Rhodococcus strains. In addition, the involvement of PAA pathway in lignin degradation can help to further improve lignin utilization, and the combinatory proteomics and bioinformatics strategies used in this study can also be applied into other systems to reveal the metabolic and regulatory pathways for balanced cellular metabolism and to select genetic targets for efficient conversion of both lignin and carbohydrates into biofuels.
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Affiliation(s)
- Xiaolu Li
- Bioproducts, Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, 2710 Crimson Way, Richland, WA 99354 USA
| | - Yucai He
- Bioproducts, Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, 2710 Crimson Way, Richland, WA 99354 USA
| | - Libing Zhang
- Bioproducts, Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, 2710 Crimson Way, Richland, WA 99354 USA
| | - Zhangyang Xu
- Bioproducts, Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, 2710 Crimson Way, Richland, WA 99354 USA
| | - Haoxi Ben
- Bioproducts, Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, 2710 Crimson Way, Richland, WA 99354 USA
| | - Matthew J. Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Yongfu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Joshua S. Yuan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77840 USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Bin Yang
- Bioproducts, Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, 2710 Crimson Way, Richland, WA 99354 USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA
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