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Czajka JJ, Han Y, Kim J, Mondo SJ, Hofstad BA, Robles A, Haridas S, Riley R, LaButti K, Pangilinan J, Andreopoulos W, Lipzen A, Yan J, Wang M, Ng V, Grigoriev IV, Spatafora JW, Magnuson JK, Baker SE, Pomraning KR. Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces. Front Bioeng Biotechnol 2024; 12:1356551. [PMID: 38638323 PMCID: PMC11024372 DOI: 10.3389/fbioe.2024.1356551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/12/2024] [Indexed: 04/20/2024] Open
Abstract
The Lipomyces clade contains oleaginous yeast species with advantageous metabolic features for biochemical and biofuel production. Limited knowledge about the metabolic networks of the species and limited tools for genetic engineering have led to a relatively small amount of research on the microbes. Here, a genome-scale metabolic model (GSM) of Lipomyces starkeyi NRRL Y-11557 was built using orthologous protein mappings to model yeast species. Phenotypic growth assays were used to validate the GSM (66% accuracy) and indicated that NRRL Y-11557 utilized diverse carbohydrates but had more limited catabolism of organic acids. The final GSM contained 2,193 reactions, 1,909 metabolites, and 996 genes and was thus named iLst996. The model contained 96 of the annotated carbohydrate-active enzymes. iLst996 predicted a flux distribution in line with oleaginous yeast measurements and was utilized to predict theoretical lipid yields. Twenty-five other yeasts in the Lipomyces clade were then genome sequenced and annotated. Sixteen of the Lipomyces species had orthologs for more than 97% of the iLst996 genes, demonstrating the usefulness of iLst996 as a broad GSM for Lipomyces metabolism. Pathways that diverged from iLst996 mainly revolved around alternate carbon metabolism, with ortholog groups excluding NRRL Y-11557 annotated to be involved in transport, glycerolipid, and starch metabolism, among others. Overall, this study provides a useful modeling tool and data for analyzing and understanding Lipomyces species metabolism and will assist further engineering efforts in Lipomyces.
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Affiliation(s)
- Jeffrey J. Czajka
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
| | - Yichao Han
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
| | - Joonhoon Kim
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, United States
| | - Stephen J. Mondo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Beth A. Hofstad
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
| | - AnaLaura Robles
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
| | - Sajeet Haridas
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - William Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Juying Yan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Mei Wang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jon K. Magnuson
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, United States
| | - Scott E. Baker
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, United States
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kyle R. Pomraning
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
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Zhou W, Wang Y, Zhang J, Zhao M, Tang M, Zhou W, Gong Z. A metabolic model of Lipomyces starkeyi for predicting lipogenesis potential from diverse low-cost substrates. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:148. [PMID: 34210354 PMCID: PMC8247262 DOI: 10.1186/s13068-021-01997-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/17/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Lipomyces starkeyi has been widely regarded as a promising oleaginous yeast with broad industrial application prospects because of its wide substrate spectrum, good adaption to fermentation inhibitors, excellent fatty acid composition for high-quality biodiesel, and negligible lipid remobilization. However, the currently low experimental lipid yield of L. starkeyi prohibits its commercial success. Metabolic model is extremely valuable to comprehend the complex biochemical processes and provide great guidance for strain modification to facilitate the lipid biosynthesis. RESULTS A small-scale metabolic model of L. starkeyi NRRL Y-11557 was constructed based on the genome annotation information. The theoretical lipid yields of glucose, cellobiose, xylose, glycerol, and acetic acid were calculated according to the flux balance analysis (FBA). The optimal flux distribution of the lipid synthesis showed that pentose phosphate pathway (PPP) independently met the necessity of NADPH for lipid synthesis, resulting in the relatively low lipid yields. Several targets (NADP-dependent oxidoreductases) beneficial for oleaginicity of L. starkeyi with significantly higher theoretical lipid yields were compared and elucidated. The combined utilization of acetic acid and other carbon sources and a hypothetical reverse β-oxidation (RBO) pathway showed outstanding potential for improving the theoretical lipid yield. CONCLUSIONS The lipid biosynthesis potential of L. starkeyi can be significantly improved through appropriate modification of metabolic network, as well as combined utilization of carbon sources according to the metabolic model. The prediction and analysis provide valuable guidance to improve lipid production from various low-cost substrates.
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Affiliation(s)
- Wei Zhou
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan, 430081 People’s Republic of China
| | - Yanan Wang
- State Key Laboratory Breeding Base of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 People’s Republic of China
| | - Junlu Zhang
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan, 430081 People’s Republic of China
| | - Man Zhao
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan, 430081 People’s Republic of China
| | - Mou Tang
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan, 430081 People’s Republic of China
| | - Wenting Zhou
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan, 430081 People’s Republic of China
- HuBei Province Key Laboratory of Coal Conversion and New Carbon Materials, Wuhan University of Science and Technology, Wuhan, 430081 People’s Republic of China
| | - Zhiwei Gong
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Road, Wuhan, 430081 People’s Republic of China
- HuBei Province Key Laboratory of Coal Conversion and New Carbon Materials, Wuhan University of Science and Technology, Wuhan, 430081 People’s Republic of China
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Bi Y, Cai S, Wang Y, Zhao X, Wang S, Xing G, Zhu Z. Structural and microbial evidence for different soil carbon sequestration after four-year successive biochar application in two different paddy soils. CHEMOSPHERE 2020; 254:126881. [PMID: 32957288 DOI: 10.1016/j.chemosphere.2020.126881] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/18/2020] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
Application of biochar (BC) derived from rice straw has generated increasing interest in long-term storage of soil organic carbon (SOC), however its carbon (C) sequestration potential vary widely among agricultural soils despite the same BC dose used. These discrepancies in the ability of soils to sequester C after BC application are poorly understood. Metabolic quotient (qCO2) is a reflection of "microbial efficiency" and linked to SOC turnover across ecosystems. Therefore, we investigated the SOC sequestration and qCO2 in a Yellow River alluvium paddy soil (YP) and a quaternary red clay paddy soil (QP) under rice-wheat annual rotation following 4-year of BC application rate of 11.3 Mg ha-1 per cropping season. BC application consistently brought 65.3 Mg C ha-1 into the soils over 4-year experimental period but increased SOC by 57.6 Mg C ha-1 in YP and 64.5 Mg C ha-1 in QP. Calculating SOC mass balance showed 11.7% of BC-C losses from YP and only 1.16% from QP. BC application stimulated the G+ bacterial, fungi, and actinomycetes by increasing O-alkyl C content in YP, while decreased the same microorganisms by decreasing anomeric C-H content in QP. Importantly, higher clay and amorphous Fe (Feo) contents in QP after BC application protected SOC from further decomposition, which in turn decreased microorganisms and resulted in higher SOC sequestration than YP. Our results indicated that soil properties controlled the extent of SOC sequestration after BC application and site-specific soil properties must be carefully considered to maximize long-term SOC sequestration after BC application.
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Affiliation(s)
- Yucui Bi
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siyuan Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xu Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Shenqiang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Guangxi Xing
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zhaoliang Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Changshu National Agro-Ecosystem Observation and Research Station, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
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Evaluation of Yarrowia lipolytica Oil for Biodiesel Production: Land Use Oil Yield, Carbon, and Energy Balance. J Lipids 2018; 2018:6393749. [PMID: 30510804 PMCID: PMC6230387 DOI: 10.1155/2018/6393749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/15/2018] [Accepted: 10/15/2018] [Indexed: 11/17/2022] Open
Abstract
Oils from yeasts have emerged as a suitable alternative raw material to produce biodiesel, due to their similar composition to common raw materials such as vegetable oils. Additionally, they have the advantage of not competing with human or animal feed, and, furthermore, they do not compete for arable land. In this work, a carbon and energy balance was evaluated for Yarrowia lipolytica as a model yeast, using crude glycerol from biodiesel as the only carbon source, which improves biodiesel overall yield by 6%. The process presented a positive energy balance. Feasibility of yeast oil as biodiesel substrate was also evaluated by determination of the lipid fatty acid profile and cetane number. Moreover, a comparison of oil yields, in terms of land use, between vegetable, microalgae, and yeast oils is also presented. The results showed that Y. lipolytica oil yield is considerably higher than vegetable oils (767 times) and microalgae (36 times).
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Simultaneous production of single cell oil and fumaric acid by a newly isolated yeast Aureobasidium pullulans var. aubasidani DH177. Bioprocess Biosyst Eng 2018; 41:1707-1716. [DOI: 10.1007/s00449-018-1994-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 07/29/2018] [Indexed: 01/24/2023]
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Islam MA, Ethiraj B, Cheng CK, Yousuf A, Thiruvenkadam S, Prasad R, Rahman Khan MM. Enhanced Current Generation Using Mutualistic Interaction of Yeast-Bacterial Coculture in Dual Chamber Microbial Fuel Cell. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.7b01855] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Amirul Islam
- Faculty
of Chemical and Natural Resources Engineering, Universiti Malaysia Pahang, 26300 Pahang, Malaysia
| | - Baranitharan Ethiraj
- Department
of Biotechnology, Bannari Amman Institute of Technology, Sathyamangalam,
Erode District, Tamil Nadu 638401, India
| | - Chin Kui Cheng
- Faculty
of Chemical and Natural Resources Engineering, Universiti Malaysia Pahang, 26300 Pahang, Malaysia
- Centre
of Excellence for advancement Research Fluid Flow (CARIFF), Universiti Malaysia Pahang, 26300 Pahang, Malaysia
| | - Abu Yousuf
- Faculty
of Engineering Technology, Universiti Malaysia Pahang, 26300 Pahang, Malaysia
| | - Selvakumar Thiruvenkadam
- Department
of Chemical and Environmental Engineering, Universiti Putra Malaysia, 43400 Serdang, Malaysia
| | - Reddy Prasad
- Department
of Petroleum and Chemical Engineering, Institut Teknologi, Gadong BE1410, Brunei
| | - Md. Maksudur Rahman Khan
- Faculty
of Chemical and Natural Resources Engineering, Universiti Malaysia Pahang, 26300 Pahang, Malaysia
- Centre
of Excellence for advancement Research Fluid Flow (CARIFF), Universiti Malaysia Pahang, 26300 Pahang, Malaysia
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Ganatsios V, Koutinas AA, Bekatorou A, Panagopoulos V, Banat IM, Terpou A, Kopsahelis N. Porous cellulose as promoter of oil production by the oleaginous yeast Lipomyces starkeyi using mixed agroindustrial wastes. BIORESOURCE TECHNOLOGY 2017; 244:629-634. [PMID: 28810217 DOI: 10.1016/j.biortech.2017.07.163] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 06/07/2023]
Abstract
Enhanced single cell oil (SCO) production by the oleaginous yeast Lipomyces starkeyi DSM 70296, immobilised on delignified porous cellulose, is reported. Pure glucose media were initially used. The effects of substrate pH and treatment temperature were evaluated, showing that 30°C and pH 5.0 were the optimum conditions for SCO production by the immobilised yeast. The immobilisation technique led to increased lipid accumulation and cell growth by 44% and 8%, respectively, in the glucose media, compared to free cells in suspension. This positive effect was also shown when low concentration mixed agro-industrial waste suspensions were used as substrates, leading to 85% enhanced SCO production in comparison with free cells. Higher fatty acid (HFA) analysis showed that yeast immobilisation led to increased formation of unsaturated HFAs (6%) and reduced saturated HFAs (5%) compared to free cells.
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Affiliation(s)
- Vassilios Ganatsios
- Department of Chemistry, University of Patras, 26500 Patras, Greece; Department of Oenology and Beverage Technology, Eastern Macedonia and Thrace Institute of Technology, 661 00 Kavala, Greece
| | | | - Argyro Bekatorou
- Department of Chemistry, University of Patras, 26500 Patras, Greece.
| | | | - Ibrahim M Banat
- School of Biomedical Sciences, University of Ulster, BT52 1SA Coleraine, N. Ireland, UK
| | - Antonia Terpou
- Department of Chemistry, University of Patras, 26500 Patras, Greece
| | - Nikolaos Kopsahelis
- Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
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Tsouko E, Kachrimanidou V, dos Santos AF, do Nascimento Vitorino Lima ME, Papanikolaou S, de Castro AM, Freire DMG, Koutinas AA. Valorization of By-Products from Palm Oil Mills for the Production of Generic Fermentation Media for Microbial Oil Synthesis. Appl Biochem Biotechnol 2016; 181:1241-1256. [DOI: 10.1007/s12010-016-2281-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/04/2016] [Indexed: 10/20/2022]
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