{"entity": "journal", "iuid": "c7c9c8e8993244d69708d6c462134514", "timestamp": "2026-09-12T07:34:48.550Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/Metab.%20Eng..json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/Metab.%20Eng."}}, "title": "Metab. Eng.", "issn": "1096-7184", "issn-l": "1096-7176", "publications_count": 16, "publications": [{"entity": "publication", "iuid": "8babe32196614e2ca44fdb409023c6ed", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8babe32196614e2ca44fdb409023c6ed.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8babe32196614e2ca44fdb409023c6ed"}}, "title": "Engineering of Saccharomyces cerevisiae for enhanced metabolic robustness and L-lactic acid production from lignocellulosic biomass.", "authors": [{"family": "Choi", "given": "Bohyun", "initials": "B"}, {"family": "Tafur Rangel", "given": "Albert", "initials": "A"}, {"family": "Kerkhoven", "given": "Eduard J", "initials": "EJ"}, {"family": "Nyg\u00e5rd", "given": "Yvonne", "initials": "Y"}], "type": "journal article", "published": "2024-07-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "volume": "84", "pages": "23-33", "issn-l": "1096-7176"}, "abstract": "Metabolic engineering for high productivity and increased robustness is needed to enable sustainable biomanufacturing of lactic acid from lignocellulosic biomass. Lactic acid is an important commodity chemical used for instance as a monomer for production of polylactic acid, a biodegradable polymer. Here, rational and model-based optimization was used to engineer a diploid, xylose fermenting Saccharomyces cerevisiae strain to produce L-lactic acid. The metabolic flux was steered towards lactic acid through the introduction of multiple lactate dehydrogenase encoding genes while deleting ERF2, GPD1, and CYB2. A production of 93 g/L of lactic acid with a yield of 0.84 g/g was achieved using xylose as the carbon source. To increase xylose utilization and reduce acetic acid synthesis, PHO13 and ALD6 were also deleted from the strain. Finally, CDC19 encoding a pyruvate kinase was overexpressed, resulting in a yield of 0.75 g lactic acid/g sugars consumed, when the substrate used was a synthetic lignocellulosic hydrolysate medium, containing hexoses, pentoses and inhibitors such as acetate and furfural. Notably, modeling also provided leads for understanding the influence of oxygen in lactic acid production. High lactic acid production from xylose, at oxygen-limitation could be explained by a reduced flux through the oxidative phosphorylation pathway. On the contrast, higher oxygen levels were beneficial for lactic acid production with the synthetic hydrolysate medium, likely as higher ATP concentrations are needed for tolerating the inhibitors therein. The work highlights the potential of S. cerevisiae for industrial production of lactic acid from lignocellulosic biomass.", "doi": "10.1016/j.ymben.2024.05.003", "pmid": "38788894", "labels": [], "xrefs": [{"db": "pii", "key": "S1096-7176(24)00069-7"}], "notes": [], "created": "2026-08-20T08:07:20.135Z", "modified": "2026-08-20T08:07:20.191Z"}, {"entity": "publication", "iuid": "8de849d479ba44e699194d67ee107204", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8de849d479ba44e699194d67ee107204.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8de849d479ba44e699194d67ee107204"}}, "title": "Tuning of CHO secretional machinery improve activity of secreted therapeutic sulfatase 150-fold.", "authors": [{"family": "Thal\u00e9n", "given": "Niklas Berndt", "initials": "NB"}, {"family": "Barzadd", "given": "Mona Moradi", "initials": "MM"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Rodhe", "given": "Johanna", "initials": "J"}, {"family": "Andersson", "given": "Monica", "initials": "M"}, {"family": "Bidkhori", "given": "Gholamreza", "initials": "G"}, {"family": "Possner", "given": "Dominik", "initials": "D"}, {"family": "Su", "given": "Chao", "initials": "C"}, {"family": "Nilsson", "given": "Joakim", "initials": "J"}, {"family": "Eisenhut", "given": "Peter", "initials": "P"}, {"family": "Malm", "given": "Magdalena", "initials": "M"}, {"family": "Karlsson", "given": "Alice", "initials": "A"}, {"family": "Vestin", "given": "Jeanette", "initials": "J"}, {"family": "Forsberg", "given": "Johan", "initials": "J"}, {"family": "Nordling", "given": "Erik", "initials": "E"}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Volk", "given": "Anna-Luisa", "initials": "AL"}, {"family": "Sandegren", "given": "Anna", "initials": "A"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2024-01-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "volume": "81", "pages": "157-166", "issn-l": "1096-7176"}, "abstract": "Rare diseases are, despite their name, collectively common and millions of people are affected daily of conditions where treatment often is unavailable. Sulfatases are a large family of activating enzymes related to several of these diseases. Heritable genetic variations in sulfatases may lead to impaired activity and a reduced macromolecular breakdown within the lysosome, with several severe and lethal conditions as a consequence. While therapeutic options are scarce, treatment for some sulfatase deficiencies by recombinant enzyme replacement are available. The recombinant production of such sulfatases suffers greatly from both low product activity and yield, further limiting accessibility for patient groups. To mitigate the low product activity, we have investigated cellular properties through computational evaluation of cultures with varying media conditions and comparison of two CHO clones with different levels of one active sulfatase variant. Transcriptome analysis identified 18 genes in secretory pathways correlating with increased sulfatase production. Experimental validation by upregulation of a set of three key genes improved the specific enzymatic activity at varying degree up to 150-fold in another sulfatase variant, broadcasting general production benefits. We also identified a correlation between product mRNA levels and sulfatase activity that generated an increase in sulfatase activity when expressed with a weaker promoter. Furthermore, we suggest that our proposed workflow for resolving bottlenecks in cellular machineries, to be useful for improvements of cell factories for other biologics as well.", "doi": "10.1016/j.ymben.2023.12.003", "pmid": "38081506", "labels": [], "xrefs": [{"db": "pii", "key": "S1096-7176(23)00176-3"}], "notes": [], "created": "2026-08-20T08:07:18.122Z", "modified": "2026-08-20T08:07:18.178Z"}, {"entity": "publication", "iuid": "387e3621f81741fca8e7892a9e66bc91", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/387e3621f81741fca8e7892a9e66bc91.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/387e3621f81741fca8e7892a9e66bc91"}}, "title": "Laboratory evolution of Synechocystis sp. PCC 6803 for phenylpropanoid production.", "authors": [{"family": "Kukil", "given": "Kateryna", "initials": "K"}, {"family": "Englund", "given": "Elias", "initials": "E"}, {"family": "Crang", "given": "Nick", "initials": "N"}, {"family": "Hudson", "given": "Elton P", "initials": "EP"}, {"family": "Lindberg", "given": "Pia", "initials": "P"}], "type": "journal article", "published": "2023-09-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "volume": "79", "pages": "27-37", "issn-l": "1096-7176"}, "abstract": "Cyanobacteria are promising as a biotechnological platform for production of various industrially relevant compounds, including aromatic amino acids and their derivatives, phenylpropanoids. In this study, we have generated phenylalanine resistant mutant strains (PRMs) of the unicellular cyanobacterium Synechocystis sp. PCC 6803, by laboratory evolution under the selective pressure of phenylalanine, which inhibits the growth of wild type Synechocystis. The new strains of Synechocystis were tested for their ability to secrete phenylalanine in the growth medium during cultivation in shake flasks as well as in a high-density cultivation (HDC) system. All PRM strains secreted phenylalanine into the culture medium, with one of the mutants, PRM8, demonstrating the highest specific production of 24.9 \u00b1 7 mg L-1\u00b7OD750-1 or 610 \u00b1 196 mg L-1 phenylalanine after four days of growth in HDC. We further overexpressed phenylalanine ammonia lyase (PAL) and tyrosine ammonia lyase (TAL) in the mutant strains in order to determine the potential of PRMs for production of trans-cinnamic acid (tCA) and para-coumaric acid (pCou), the first intermediates of the plant phenylpropanoid pathway. Productivities of these compounds were found to be lower in the PRMs compared to respective control strains, except for PRM8 under HDC conditions. The PRM8 background strain in combination with PAL or TAL expression demonstrated a specific production of 52.7 \u00b1 15 mg L-1\u00b7OD750-1tCA and 47.1 \u00b1 7 mg L-1\u00b7OD750-1pCou, respectively, with a volumetric titer reaching above 1 g L-1 for both products after four days of HDC cultivation. The genomes of PRMs were sequenced in order to identify which mutations caused the phenotype. Interestingly, all of the PRMs contained at least one mutation in their ccmA gene, which encodes DAHP synthase, the first enzyme of the pathway for aromatic amino acids biosynthesis. Altogether, we demonstrate that the combination of laboratory-evolved mutants and targeted metabolic engineering can be a powerful tool in cyanobacterial strain development.", "doi": "10.1016/j.ymben.2023.06.014", "pmid": "37392984", "labels": [], "xrefs": [{"db": "pii", "key": "S1096-7176(23)00096-4"}], "notes": [], "created": "2026-08-20T08:07:15.408Z", "modified": "2026-08-20T08:07:15.421Z"}, {"entity": "publication", "iuid": "74bcd441a88b4f10b039caeb57649cf5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/74bcd441a88b4f10b039caeb57649cf5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/74bcd441a88b4f10b039caeb57649cf5"}}, "title": "Thermodynamic limitations of PHB production from formate and fructose in Cupriavidus necator.", "authors": [{"family": "Janasch", "given": "Markus", "initials": "M"}, {"family": "Crang", "given": "Nick", "initials": "N"}, {"family": "Asplund-Samuelsson", "given": "Johannes", "initials": "J"}, {"family": "Sporre", "given": "Emil", "initials": "E"}, {"family": "Bruch", "given": "Manuel", "initials": "M"}, {"family": "Gynn\u00e5", "given": "Arvid", "initials": "A"}, {"family": "Jahn", "given": "Michael", "initials": "M"}, {"family": "Hudson", "given": "Elton P", "initials": "EP"}], "type": "journal article", "published": "2022-09-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "volume": "73", "pages": "256-269", "issn-l": "1096-7176"}, "abstract": "The chemolithotroph Cupriavidus necator H16 is known as a natural producer of the bioplastic-polymer PHB, as well as for its metabolic versatility to utilize different substrates, including formate as the sole carbon and energy source. Depending on the entry point of the substrate, this versatility requires adjustment of the thermodynamic landscape to maintain sufficiently high driving forces for biological processes. Here we employed a model of the core metabolism of C. necator H16 to analyze the thermodynamic driving forces and PHB yields from formate for different metabolic engineering strategies. For this, we enumerated elementary flux modes (EFMs) of the network and evaluated their PHB yields as well as thermodynamics via Max-min driving force (MDF) analysis and random sampling of driving forces. A heterologous ATP:citrate lyase reaction was predicted to increase driving force for producing acetyl-CoA. A heterologous phosphoketolase reaction was predicted to increase maximal PHB yields as well as driving forces. These enzymes were then verified experimentally to enhance PHB titers between 60 and 300% in select conditions. The EFM analysis also revealed that PHB production from formate may be limited by low driving forces through citrate lyase and aconitase, as well as cofactor balancing, and identified additional reactions associated with low and high PHB yield. Proteomics analysis of the engineered strains confirmed an increased abundance of aconitase and cofactor balancing. The findings of this study aid in understanding metabolic adaptation. Furthermore, the outlined approach will be useful in designing metabolic engineering strategies in other non-model bacteria.", "doi": "10.1016/j.ymben.2022.08.005", "pmid": "35987434", "labels": [], "xrefs": [{"db": "pii", "key": "S1096-7176(22)00100-8"}], "notes": [], "created": "2026-08-20T08:07:13.277Z", "modified": "2026-08-20T08:07:13.328Z"}, {"entity": "publication", "iuid": "37d7ec646f7641f299ef896938cd56e6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/37d7ec646f7641f299ef896938cd56e6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/37d7ec646f7641f299ef896938cd56e6"}}, "title": "Synthetic metabolic pathways for conversion of CO2 into secreted short-to medium-chain hydrocarbons using cyanobacteria.", "authors": [{"family": "Yunus", "given": "Ian S", "initials": "IS"}, {"family": "Anfelt", "given": "Josefine", "initials": "J"}, {"family": "Sporre", "given": "Emil", "initials": "E"}, {"family": "Miao", "given": "Rui", "initials": "R"}, {"family": "Hudson", "given": "Elton P", "initials": "EP"}, {"family": "Jones", "given": "Patrik R", "initials": "PR"}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "volume": "72", "pages": "14-23", "issn-l": "1096-7176"}, "abstract": "The objective of this study was to implement direct sunlight-driven conversion of CO2 into a naturally excreted ready-to-use fuel. We engineered four different synthetic metabolic modules for biosynthesis of short-to medium-chain length hydrocarbons in the model cyanobacterium Synechocystis sp. PCC 6803. In module 1, the combination of a truncated clostridial n-butanol pathway with over-expression of the native cyanobacterial aldehyde deformylating oxygenase resulted in small quantities of propane when cultured under closed conditions. Direct conversion of CO2 into propane was only observed in strains with CRISPRi-mediated repression of three native putative aldehyde reductases. In module 2, three different pathways towards pentane were evaluated based on the polyunsaturated fatty acid linoleic acid as an intermediate. Through combinatorial evaluation of reaction ingredients, it was concluded that linoleic acid undergoes a spontaneous non-enzymatic reaction to yield pentane and hexanal. When Synechocystis was added to the reaction, hexanal was converted into 1-hexanol, but there was no further stimulation of pentane biosynthesis even in the Synechocystis strains expressing GmLOX1. For modules 3 and 4, several different acyl-ACP thioesterases were evaluated in combination with two different decarboxylases. Small quantities of 1-heptene and 1-nonene were observed in strains expressing the desaturase-like enzyme UndB from Pseudomonas mendocina in combination with C8-C10 preferring thioesterases ('CaFatB3.5 and 'ChoFatB2.2). When UndB instead was combined with a C12-specific 'UcFatB1 thioesterase, this resulted in a ten-fold increase of alkene biosynthesis. When UndB was replaced with the light-dependent FAP decarboxylase, both undecane and tridecane accumulated, albeit with a 10-fold drop in productivity. Preliminary optimization of the RBS, promoter and gene order in some of the synthetic operons resulted in improved 1-alkene productivity, reaching a titer of 230 mg/L after 10 d with 15% carbon partitioning. In conclusion, the direct bioconversion of CO2 into secreted and ready-to-use hydrocarbon fuel was implemented with several different metabolic systems. Optimal productivity was observed with UndB and a C12 chain-length specific thioesterase, although further optimization of the entire biosynthetic system is still possible.", "doi": "10.1016/j.ymben.2022.01.017", "pmid": "35134557", "labels": [], "xrefs": [{"db": "pii", "key": "S1096-7176(22)00023-4"}], "notes": [], "created": "2026-08-20T08:07:09.348Z", "modified": "2026-08-20T08:07:09.379Z"}, {"entity": "publication", "iuid": "a262c24ffd2e4b568f79c6a4399bc8be", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a262c24ffd2e4b568f79c6a4399bc8be.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a262c24ffd2e4b568f79c6a4399bc8be"}}, "title": "Harnessing secretory pathway differences between HEK293 and CHO to rescue production of difficult to express proteins.", "authors": [{"family": "Malm", "given": "Magdalena", "initials": "M"}, {"family": "Kuo", "given": "Chih-Chung", "initials": "CC"}, {"family": "Barzadd", "given": "Mona Moradi", "initials": "MM"}, {"family": "Mebrahtu", "given": "Aman", "initials": "A"}, {"family": "Wistbacka", "given": "Num", "initials": "N"}, {"family": "Razavi", "given": "Ronia", "initials": "R"}, {"family": "Volk", "given": "Anna-Luisa", "initials": "AL"}, {"family": "Lundqvist", "given": "Magnus", "initials": "M"}, {"family": "Kotol", "given": "David", "initials": "D"}, {"family": "Tegel", "given": "Hanna", "initials": "H"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Gr\u00e4slund", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Chotteau", "given": "Veronique", "initials": "V"}, {"family": "Field", "given": "Ray", "initials": "R"}, {"family": "Varley", "given": "Paul G", "initials": "PG"}, {"family": "Roth", "given": "Robert G", "initials": "RG"}, {"family": "Lewis", "given": "Nathan E", "initials": "NE"}, {"family": "Hatton", "given": "Diane", "initials": "D"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2022-07-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "volume": "72", "pages": "171-187", "issn-l": "1096-7176"}, "abstract": "Biologics represent the fastest growing group of therapeutics, but many advanced recombinant protein moieties remain difficult to produce. Here, we identify metabolic engineering targets limiting expression of recombinant human proteins through a systems biology analysis of the transcriptomes of CHO and HEK293 during recombinant expression. In an expression comparison of 24 difficult to express proteins, one third of the challenging human proteins displayed improved secretion upon host cell swapping from CHO to HEK293. Guided by a comprehensive transcriptomics comparison between cell lines, especially highlighting differences in secretory pathway utilization, a co-expression screening of 21 secretory pathway components validated ATF4, SRP9, JUN, PDIA3 and HSPA8 as productivity boosters in CHO. Moreover, more heavily glycosylated products benefitted more from the elevated activities of the N- and O-glycosyltransferases found in HEK293. Collectively, our results demonstrate the utilization of HEK293 for expression rescue of human proteins and suggest a methodology for identification of secretory pathway components for metabolic engineering of HEK293 and CHO.", "doi": "10.1016/j.ymben.2022.03.009", "pmid": "35301123", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1801357"}, {"db": "pmc", "key": "PMC9189052"}, {"db": "pii", "key": "S1096-7176(22)00044-1"}], "notes": [], "created": "2026-08-20T08:07:11.071Z", "modified": "2026-08-20T08:07:11.116Z"}, {"entity": "publication", "iuid": "65dd3cf48c0540c297aff6254dfbcca9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/65dd3cf48c0540c297aff6254dfbcca9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/65dd3cf48c0540c297aff6254dfbcca9"}}, "title": "Cycling between growth and production phases increases cyanobacteria bioproduction of lactate.", "authors": [{"family": "Shabestary", "given": "Kiyan", "initials": "K"}, {"family": "Hern\u00e1ndez", "given": "Hugo Pineda", "initials": "HP"}, {"family": "Miao", "given": "Rui", "initials": "R"}, {"family": "Ljungqvist", "given": "Emil", "initials": "E"}, {"family": "Hallman", "given": "Olivia", "initials": "O"}, {"family": "Sporre", "given": "Emil", "initials": "E"}, {"family": "Branco Dos Santos", "given": "Filipe", "initials": "F"}, {"family": "Hudson", "given": "Elton P", "initials": "EP"}], "type": "journal article", "published": "2021-11-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "volume": "68", "pages": "131-141", "issn-l": "1096-7176"}, "abstract": "Decoupling growth from product synthesis is a promising strategy to increase carbon partitioning and maximize productivity in cell factories. However, reduction in both substrate uptake rate and metabolic activity in the production phase are an underlying problem for upscaling. Here, we used CRISPR interference to repress growth in lactate-producing Synechocystis sp. PCC 6803. Carbon partitioning to lactate in the production phase exceeded 90%, but CO2 uptake was severely reduced compared to uptake during the growth phase. We characterized strains during the onset of growth arrest using transcriptomics and proteomics. Multiple genes involved in ATP homeostasis were regulated once growth was inhibited, which suggests an alteration of energy charge that may lead to reduced substrate uptake. In order to overcome the reduced metabolic activity and take advantage of increased carbon partitioning, we tested a novel production strategy that involved alternating growth arrest and recovery by periodic addition of an inducer molecule to activate CRISPRi. Using this strategy, we maintained lactate biosynthesis in Synechocystis for 30 days in a constant light turbidostat cultivation. Cumulative lactate titers were also increased by 100% compared to a constant growth-arrest regime, and reached 1 g/L. Further, the cultivation produced lactate for 30 days, compared to 20 days for the non-growth arrest cultivation. Periodic growth arrest could be applicable for other products, and in cyanobacteria, could be linked to internal circadian rhythms that persist in constant light.", "doi": "10.1016/j.ymben.2021.09.010", "pmid": "34601120", "labels": [], "xrefs": [{"db": "pii", "key": "S1096-7176(21)00150-6"}], "notes": [], "created": "2026-08-20T08:07:00.152Z", "modified": "2026-08-20T08:07:00.205Z"}, {"entity": "publication", "iuid": "fb746087a9c94556b5a56a862e9e9b1f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/fb746087a9c94556b5a56a862e9e9b1f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/fb746087a9c94556b5a56a862e9e9b1f"}}, "title": "Pyruvate kinase L/R is a regulator of lipid metabolism and mitochondrial function.", "authors": [{"family": "Liu", "given": "Zhengtao", "initials": "Z"}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Lee", "given": "Sunjae", "initials": "S"}, {"family": "Kim", "given": "Woonghee", "initials": "W"}, {"family": "Klevstig", "given": "Martina", "initials": "M", "orcid": "0000-0001-7563-4161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/eac579cfda084526988ba438919e8b5f.json"}}, {"family": "Harzandi", "given": "Azadeh M", "initials": "AM"}, {"family": "Sikanic", "given": "Natasa", "initials": "N"}, {"family": "Arif", "given": "Muhammad", "initials": "M"}, {"family": "St\u00e5hlman", "given": "Marcus", "initials": "M"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Boren", "given": "Jan", "initials": "J", "orcid": "0000-0003-0786-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73a770eb9e614448a046b8e9199052e9.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}], "type": "journal article", "published": "2019-03-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "issn-l": "1096-7176", "volume": "52", "issue": null, "pages": "263-272"}, "abstract": "The pathogenesis of non-alcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC) has been associated with altered expression of liver-specific genes including pyruvate kinase liver and red blood cell (PKLR), patatin-like phospholipase domain containing 3 (PNPLA3) and proprotein convertase subtilisin/kexin type 9 (PCSK9). Here, we inhibited and overexpressed the expression of these three genes in HepG2 cells, generated RNA-seq data before and after perturbation and revealed the altered global biological functions with the modulation of these genes using integrated network (IN) analysis. We found that modulation of these genes effects the total triglycerides levels within the cells and viability of the cells. Next, we generated IN for HepG2 cells, identified reporter transcription factors based on IN and found that the modulation of these genes affects key metabolic pathways associated with lipid metabolism (steroid biosynthesis, PPAR signalling pathway, fatty acid synthesis and oxidation) and cancer development (DNA replication, cell cycle and p53 signalling) involved in the progression of NAFLD and HCC. Finally, we observed that inhibition of PKLR lead to decreased glucose uptake and decreased mitochondrial activity in HepG2 cells. Hence, our systems level analysis indicated that PKLR can be targeted for development efficient treatment strategy for NAFLD and HCC.", "doi": "10.1016/j.ymben.2019.01.001", "pmid": "30615941", "labels": {"Adil Mardinoglu": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "S1096-7176(18)30318-5"}], "notes": [], "created": "2020-09-25T13:17:30.855Z", "modified": "2022-11-04T11:32:16.691Z"}, {"entity": "publication", "iuid": "07ad640e3e47469eb45e93e1342c6173", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/07ad640e3e47469eb45e93e1342c6173.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/07ad640e3e47469eb45e93e1342c6173"}}, "title": "Systematic overexpression study to find target enzymes enhancing production of terpenes in Synechocystis PCC 6803, using isoprene as a model compound.", "authors": [{"family": "Englund", "given": "Elias", "initials": "E"}, {"family": "Shabestary", "given": "Kiyan", "initials": "K"}, {"family": "Hudson", "given": "Elton P", "initials": "EP"}, {"family": "Lindberg", "given": "Pia", "initials": "P"}], "type": "journal article", "published": "2018-09-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "issn-l": "1096-7176", "volume": "49", "issue": null, "pages": "164-177"}, "abstract": "Of the two natural metabolic pathways for making terpenoids, biotechnological utilization of the mevalonate (MVA) pathway has enabled commercial production of valuable compounds, while the more recently discovered but stoichiometrically more efficient methylerythritol phosphate (MEP) pathway is underdeveloped. We conducted a study on the overexpression of each enzyme in the MEP pathway in the unicellular cyanobacterium Synechocystis sp. PCC 6803, to identify potential targets for increasing flux towards terpenoid production, using isoprene as a reporter molecule. Results showed that the enzymes Ipi, Dxs and IspD had the biggest impact on isoprene production. By combining and creating operons out of those genes, isoprene production was increased 2-fold compared to the base strain. A genome-scale model was used to identify targets upstream of the MEP pathway that could redirect flux towards terpenoids. A total of ten reactions from the Calvin-Benson-Bassham cycle, lower glycolysis and co-factor synthesis pathways were probed for their effect on isoprene synthesis by co-expressing them with the MEP enzymes, resulting in a 60% increase in production from the best strain. Lastly, we studied two isoprene synthases with the highest reported catalytic rates. Only by expressing them together with Dxs and Ipi could we get stable strains that produced 2.8 mg/g isoprene per dry cell weight, a 40-fold improvement compared to the initial strain.", "doi": "10.1016/j.ymben.2018.07.004", "pmid": "30025762", "labels": {"Paul Hudson": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "S1096-7176(18)30143-5"}], "notes": [], "created": "2020-10-06T14:20:31.519Z", "modified": "2022-11-04T11:32:17.313Z"}, {"entity": "publication", "iuid": "1cb2224619c048a2aa17135b4df3459e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1cb2224619c048a2aa17135b4df3459e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1cb2224619c048a2aa17135b4df3459e"}}, "title": "Heterologous transporter expression for improved fatty alcohol secretion in yeast.", "authors": [{"family": "Hu", "given": "Yating", "initials": "Y"}, {"family": "Zhu", "given": "Zhiwei", "initials": "Z"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Siewers", "given": "Verena", "initials": "V"}], "type": "journal article", "published": "2018-01-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "volume": "45", "issue": null, "pages": "51-58", "issn-l": "1096-7176"}, "abstract": "The yeast Saccharomyces cerevisiae is an attractive host for industrial scale production of biofuels including fatty alcohols due to its robustness and tolerance towards harsh fermentation conditions. Many metabolic engineering strategies have been applied to generate high fatty alcohol production strains. However, impaired growth caused by fatty alcohol accumulation and high cost of extraction are factors limiting large-scale production. Here, we demonstrate that the use of heterologous transporters is a promising strategy to increase fatty alcohol production. Among several plant and mammalian transporters tested, human FATP1 was shown to mediate fatty alcohol export in a high fatty alcohol production yeast strain. An approximately five-fold increase of fatty alcohol secretion was achieved. The results indicate that the overall cell fitness benefited from fatty alcohol secretion and that the acyl-CoA synthase activity of FATP1 contributed to increased cell growth as well. This is the first study that enabled an increased cell fitness for fatty alcohol production by heterologous transporter expression in yeast, and this investigation indicates a new potential function of FATP1, which has been known as a free fatty acid importer to date. We furthermore successfully identified the functional domain of FATP1 involved in fatty alcohol export through domain exchange between FATP1 and another transporter, FATP4. This study may facilitate a successful commercialization of fatty alcohol production in yeast and inspire the design of novel cell factories.", "doi": "10.1016/j.ymben.2017.11.008", "pmid": "29183749", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "S1096-7176(17)30295-1"}], "notes": [], "created": "2018-12-05T12:49:02.769Z", "modified": "2018-12-05T12:49:02.787Z"}, {"entity": "publication", "iuid": "8890a179e15141cabee6c0b0066858b3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8890a179e15141cabee6c0b0066858b3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8890a179e15141cabee6c0b0066858b3"}}, "title": "Diversion of the long-chain acyl-ACP pool in Synechocystis to fatty alcohols through CRISPRi repression of the essential phosphate acyltransferase PlsX.", "authors": [{"family": "Kaczmarzyk", "given": "Danuta", "initials": "D"}, {"family": "Cengic", "given": "Ivana", "initials": "I"}, {"family": "Yao", "given": "Lun", "initials": "L"}, {"family": "Hudson", "given": "Elton P", "initials": "EP"}], "type": "journal article", "published": "2018-01-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "issn-l": "1096-7176", "volume": "45", "issue": null, "pages": "59-66"}, "abstract": "Fatty alcohol production in Synechocystis sp. PCC 6803 was achieved through heterologous expression of the fatty acyl-CoA/ACP reductase Maqu2220 from the bacteria Marinobacter aquaeolei VT8 and the fatty acyl-ACP reductase DPW from the rice Oryza sativa. These platform strains became models for testing multiplex CRISPR-interference (CRISPRi) metabolic engineering strategies to both improve fatty alcohol production and to study membrane homeostasis. CRISPRi allowed partial repression of up to six genes simultaneously, each encoding enzymes of acyl-ACP-consuming pathways. We identified the essential phosphate acyltransferase enzyme PlsX (slr1510) as a key node in C18 fatty acyl-ACP consumption, repression of slr1510 increased octadecanol productivity threefold over the base strain and gave the highest specific titers reported for this host, 10.3mgg-1 DCW. PlsX catalyzes the first committed step of phosphatidic acid synthesis, and has not been characterized in Synechocystis previously. We found that accumulation of fatty alcohols impaired growth, altered the membrane composition, and caused a build-up of reactive oxygen species.", "doi": "10.1016/j.ymben.2017.11.014", "pmid": "29199103", "labels": {"Affiliated researcher": null, "Paul Hudson": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "S1096-7176(17)30383-X"}], "notes": [], "created": "2018-12-03T14:44:45.870Z", "modified": "2022-11-04T11:32:18.222Z"}, {"entity": "publication", "iuid": "88ca529696bd4dca8a148caed0892992", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/88ca529696bd4dca8a148caed0892992.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/88ca529696bd4dca8a148caed0892992"}}, "title": "Thermodynamic analysis of computed pathways integrated into the metabolic networks of E. coli and Synechocystis reveals contrasting expansion potential.", "authors": [{"family": "Asplund-Samuelsson", "given": "Johannes", "initials": "J"}, {"family": "Janasch", "given": "Markus", "initials": "M"}, {"family": "Hudson", "given": "Elton P", "initials": "EP"}], "type": "journal article", "published": "2018-01-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "issn-l": "1096-7176", "volume": "45", "issue": null, "pages": "223-236"}, "abstract": "Introducing biosynthetic pathways into an organism is both reliant on and challenged by endogenous biochemistry. Here we compared the expansion potential of the metabolic network in the photoautotroph Synechocystis with that of the heterotroph E. coli using the novel workflow POPPY (Prospecting Optimal Pathways with PYthon). First, E. coli and Synechocystis metabolomic and fluxomic data were combined with metabolic models to identify thermodynamic constraints on metabolite concentrations (NET analysis). Then, thousands of automatically constructed pathways were placed within each network and subjected to a network-embedded variant of the max-min driving force analysis (NEM). We found that the networks had different capabilities for imparting thermodynamic driving forces toward certain compounds. Key metabolites were constrained differently in Synechocystis due to opposing flux directions in glycolysis and carbon fixation, the forked tri-carboxylic acid cycle, and photorespiration. Furthermore, the lysine biosynthesis pathway in Synechocystis was identified as thermodynamically constrained, impacting both endogenous and heterologous reactions through low 2-oxoglutarate levels. Our study also identified important yet poorly covered areas in existing metabolomics data and provides a reference for future thermodynamics-based engineering in Synechocystis and beyond. The POPPY methodology represents a step in making optimal pathway-host matches, which is likely to become important as the practical range of host organisms is diversified.", "doi": "10.1016/j.ymben.2017.12.011", "pmid": "29278749", "labels": {"Affiliated researcher": null, "Paul Hudson": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "S1096-7176(17)30107-6"}], "notes": [], "created": "2018-12-03T14:44:49.265Z", "modified": "2022-11-04T11:32:18.116Z"}, {"entity": "publication", "iuid": "f3f96f7da5274f03af18e2b2dc108865", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f3f96f7da5274f03af18e2b2dc108865.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f3f96f7da5274f03af18e2b2dc108865"}}, "title": "Enabling the synthesis of medium chain alkanes and 1-alkenes in yeast.", "authors": [{"family": "Zhu", "given": "Zhiwei", "initials": "Z"}, {"family": "Zhou", "given": "Yongjin J", "initials": "YJ"}, {"family": "Kang", "given": "Min-Kyoung", "initials": "MK"}, {"family": "Krivoruchko", "given": "Anastasia", "initials": "A"}, {"family": "Buijs", "given": "Nicolaas A", "initials": "NA"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}], "type": "journal article", "published": "2017-11-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "volume": "44", "issue": null, "pages": "81-88", "issn-l": "1096-7176"}, "abstract": "Microbial synthesis of medium chain aliphatic hydrocarbons, attractive drop-in molecules to gasoline and jet fuels, is a promising way to reduce our reliance on petroleum-based fuels. In this study, we enabled the synthesis of straight chain hydrocarbons (C7-C13) by yeast Saccharomyces cerevisiae through engineering fatty acid synthases to control the chain length of fatty acids and introducing heterologous pathways for alkane or 1-alkene synthesis. We carried out enzyme engineering/screening of the fatty aldehyde deformylating oxygenase (ADO), and compartmentalization of the alkane biosynthesis pathway into peroxisomes to improve alkane production. The two-step synthesis of alkanes was found to be inefficient due to the formation of alcohols derived from aldehyde intermediates. Alternatively, the drain of aldehyde intermediates could be circumvented by introducing a one-step decarboxylation of fatty acids to 1-alkenes, which could be synthesized at a level of 3mg/L, 25-fold higher than that of alkanes produced via aldehydes.", "doi": "10.1016/j.ymben.2017.09.007", "pmid": "28939277", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "S1096-7176(17)30126-X"}], "notes": [], "created": "2018-12-05T11:35:41.211Z", "modified": "2018-12-05T11:35:41.230Z"}, {"entity": "publication", "iuid": "3dd620737efa46b0bd712c488765d3b8", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3dd620737efa46b0bd712c488765d3b8.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3dd620737efa46b0bd712c488765d3b8"}}, "title": "Genome scale metabolic modeling of cancer.", "authors": [{"family": "Nilsson", "given": "Avlant", "initials": "A", "orcid": "0000-0002-9476-4516", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f2e21dbc1c624f6a841c59e959e948e4.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f2b49a39ed4e54ba77dfe397ed3087.json"}}], "type": "journal article", "published": "2017-09-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "issn-l": "1096-7176", "volume": "43", "issue": "Pt B", "pages": "103-112"}, "abstract": "Cancer cells reprogram metabolism to support rapid proliferation and survival. Energy metabolism is particularly important for growth and genes encoding enzymes involved in energy metabolism are frequently altered in cancer cells. A genome scale metabolic model (GEM) is a mathematical formalization of metabolism which allows simulation and hypotheses testing of metabolic strategies. It has successfully been applied to many microorganisms and is now used to study cancer metabolism. Generic models of human metabolism have been reconstructed based on the existence of metabolic genes in the human genome. Cancer specific models of metabolism have also been generated by reducing the number of reactions in the generic model based on high throughput expression data, e.g. transcriptomics and proteomics. Targets for drugs and bio markers for diagnostics have been identified using these models. They have also been used as scaffolds for analysis of high throughput data to allow mechanistic interpretation of changes in expression. Finally, GEMs allow quantitative flux predictions using flux balance analysis (FBA). Here we critically review the requirements for successful FBA simulations of cancer cells and discuss the symmetry between the methods used for modeling of microbial and cancer metabolism. GEMs have great potential for translational research on cancer and will therefore become of increasing importance in the future.", "doi": "10.1016/j.ymben.2016.10.022", "pmid": "27825806", "labels": {"Avlant Nilsson": null, "DDLS Fellow": null}, "xrefs": [{"db": "pii", "key": "S1096-7176(16)30212-9"}], "notes": [], "created": "2025-03-20T11:06:20.312Z", "modified": "2025-03-21T13:15:02.826Z"}, {"entity": "publication", "iuid": "4e73963fb2e94117862b5591fd0b3fec", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4e73963fb2e94117862b5591fd0b3fec.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4e73963fb2e94117862b5591fd0b3fec"}}, "title": "Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments.", "authors": [{"family": "Fletcher", "given": "Eugene", "initials": "E"}, {"family": "Feizi", "given": "Amir", "initials": "A"}, {"family": "Bisschops", "given": "Markus M M", "initials": "MMM"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Khoomrung", "given": "Sakda", "initials": "S"}, {"family": "Siewers", "given": "Verena", "initials": "V"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}], "type": "journal article", "published": "2017-01-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "volume": "39", "issue": null, "pages": "19-28", "issn-l": "1096-7176"}, "abstract": "Tolerance of yeast to acid stress is important for many industrial processes including organic acid production. Therefore, elucidating the molecular basis of long term adaptation to acidic environments will be beneficial for engineering production strains to thrive under such harsh conditions. Previous studies using gene expression analysis have suggested that both organic and inorganic acids display similar responses during short term exposure to acidic conditions. However, biological mechanisms that will lead to long term adaptation of yeast to acidic conditions remains unknown and whether these mechanisms will be similar for tolerance to both organic and inorganic acids is yet to be explored. We therefore evolved Saccharomyces cerevisiae to acquire tolerance to HCl (inorganic acid) and to 0.3M L-lactic acid (organic acid) at pH 2.8 and then isolated several low pH tolerant strains. Whole genome sequencing and RNA-seq analysis of the evolved strains revealed different sets of genome alterations suggesting a divergence in adaptation to these two acids. An altered sterol composition and impaired iron uptake contributed to HCl tolerance whereas the formation of a multicellular morphology and rapid lactate degradation was crucial for tolerance to high concentrations of lactic acid. Our findings highlight the contribution of both the selection pressure and nature of the acid as a driver for directing the evolutionary path towards tolerance to low pH. The choice of carbon source was also an important factor in the evolutionary process since cells evolved on two different carbon sources (raffinose and glucose) generated a different set of mutations in response to the presence of lactic acid. Therefore, different strategies are required for a rational design of low pH tolerant strains depending on the acid of interest.", "doi": "10.1016/j.ymben.2016.10.010", "pmid": "27815194", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pii", "key": "S1096-7176(16)30175-6"}], "notes": [], "created": "2018-12-05T11:27:26.875Z", "modified": "2018-12-05T11:27:26.894Z"}, {"entity": "publication", "iuid": "8a48f5c8741d490f89b58ca81df73321", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8a48f5c8741d490f89b58ca81df73321.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8a48f5c8741d490f89b58ca81df73321"}}, "title": "Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance.", "authors": [{"family": "Kildegaard", "given": "Kanchana R", "initials": "KR"}, {"family": "Hallstr\u00f6m", "given": "Bj\u00f6rn M", "initials": "BM"}, {"family": "Blicher", "given": "Thomas H", "initials": "TH"}, {"family": "Sonnenschein", "given": "Nikolaus", "initials": "N"}, {"family": "Jensen", "given": "Niels B", "initials": "NB"}, {"family": "Sherstyk", "given": "Svetlana", "initials": "S"}, {"family": "Harrison", "given": "Scott J", "initials": "SJ"}, {"family": "Maury", "given": "J\u00e9r\u00f4me", "initials": "J"}, {"family": "Herrg\u00e5rd", "given": "Markus J", "initials": "MJ"}, {"family": "Juncker", "given": "Agnieszka S", "initials": "AS"}, {"family": "Forster", "given": "Jochen", "initials": "J"}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Borodina", "given": "Irina", "initials": "I"}], "type": "journal article", "published": "2014-11-00", "journal": {"title": "Metab. Eng.", "issn": "1096-7184", "volume": "26", "issue": null, "pages": "57-66", "issn-l": "1096-7176"}, "abstract": "Biologically produced 3-hydroxypropionic acid (3 HP) is a potential source for sustainable acrylates and can also find direct use as monomer in the production of biodegradable polymers. For industrial-scale production there is a need for robust cell factories tolerant to high concentration of 3 HP, preferably at low pH. Through adaptive laboratory evolution we selected S. cerevisiae strains with improved tolerance to 3 HP at pH 3.5. Genome sequencing followed by functional analysis identified the causal mutation in SFA1 gene encoding S-(hydroxymethyl)glutathione dehydrogenase. Based on our findings, we propose that 3 HP toxicity is mediated by 3-hydroxypropionic aldehyde (reuterin) and that glutathione-dependent reactions are used for reuterin detoxification. The identified molecular response to 3 HP and reuterin may well be a general mechanism for handling resistance to organic acid and aldehydes by living cells.", "doi": "10.1016/j.ymben.2014.09.004", "pmid": "25263954", "labels": [], "xrefs": [{"db": "pii", "key": "S1096-7176(14)00118-9"}], "notes": [], "created": "2018-12-05T09:24:45.303Z", "modified": "2026-08-21T11:31:41.578Z"}], "created": "2018-12-05T09:24:45.325Z", "modified": "2020-11-27T13:12:52.462Z"}