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FEMS Microbiology Reviews Aug 2021Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in... (Review)
Review
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
Topics: Arabinose; Biofuels; Pentoses; Saccharomyces cerevisiae; Xylose
PubMed: 33316044
DOI: 10.1093/femsre/fuaa069 -
Biotechnology Journal Jan 2019Extending the host substrate range of industrially relevant microbes, such as Saccharomyces cerevisiae, has been a highly-active area of research since the conception of... (Review)
Review
Extending the host substrate range of industrially relevant microbes, such as Saccharomyces cerevisiae, has been a highly-active area of research since the conception of metabolic engineering. Yet, rational strategies that enable non-native substrate utilization in this yeast without the need for combinatorial and/or evolutionary techniques are underdeveloped. Herein, this review focuses on pentose metabolism in S. cerevisiae as a case study to highlight the challenges in this field. In the last three decades, work has focused on expressing exogenous pentose metabolizing enzymes as well as endogenous enzymes for effective pentose assimilation, growth, and biofuel production. The engineering strategies that are employed for pentose assimilation in this yeast are reviewed, and compared with metabolism and regulation of native sugar, galactose. In the case of galactose metabolism, multiple signals regulate and aid growth in the presence of the sugar. However, for pentoses that are non-native, it is unclear if similar growth and regulatory signals are activated. Such a comparative analysis aids in identifying missing links in xylose and arabinose utilization. While research on pentose metabolism have mostly concentrated on pathway level optimization, recent transcriptomics analyses highlight the need to consider more global regulatory, structural, and signaling components.
Topics: Arabinose; Galactose; Metabolic Engineering; Pentoses; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Systems Biology
PubMed: 30171750
DOI: 10.1002/biot.201800364 -
Advances in Applied Microbiology 1993
Review
Topics: Acids; Bacteria; Biotechnology; Fermentation; Fungi; Pentoses; Solvents
PubMed: 8213307
DOI: 10.1016/s0065-2164(08)70594-x -
Bioresource Technology Dec 2018Most of the crop plants contain about 30% of hemicelluloses comprising D-xylose and D-arabinose. One of the major limitation for the use of pentose sugars is that high... (Review)
Review
Most of the crop plants contain about 30% of hemicelluloses comprising D-xylose and D-arabinose. One of the major limitation for the use of pentose sugars is that high purity grade D-xylose and D-arabinose are yet to be produced as commodity chemicals. Research and developmental activities are going on in this direction for their use as platform intermediates through economically viable strategies. During chemical pretreatment of biomass, the pentose sugars were generated in the liquid stream along with other compounds. This contains glucose, proteins, phenolic compounds, minerals and acids other than pentose sugars. Arabinose is present in small amounts, which can be used for the economic production of value added compound, xylitol. The present review discusses the recent trends and developments as well as challenges and opportunities in the utilization of pentose sugars generated from lignocellulosic biomass for the production of value added compounds.
Topics: Arabinose; Biofuels; Fermentation; Pentoses; Sugars; Xylose
PubMed: 30217725
DOI: 10.1016/j.biortech.2018.08.042 -
Nature Metabolism Apr 2023
Topics: Pentoses; Oxidation-Reduction; Phosphates
PubMed: 37024755
DOI: 10.1038/s42255-021-00523-3 -
Communications Biology Nov 2022Bacteria and Eucarya utilize the non-oxidative pentose phosphate pathway to direct the ribose moieties of nucleosides to central carbon metabolism. Many archaea do not...
Bacteria and Eucarya utilize the non-oxidative pentose phosphate pathway to direct the ribose moieties of nucleosides to central carbon metabolism. Many archaea do not possess this pathway, and instead, Thermococcales utilize a pentose bisphosphate pathway involving ribose-1,5-bisphosphate (R15P) isomerase and ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco). Intriguingly, multiple genomes from halophilic archaea seem only to harbor R15P isomerase, and do not harbor Rubisco. In this study, we identify a previously unrecognized nucleoside degradation pathway in halophilic archaea, composed of guanosine phosphorylase, ATP-dependent ribose-1-phosphate kinase, R15P isomerase, RuBP phosphatase, ribulose-1-phosphate aldolase, and glycolaldehyde reductase. The pathway converts the ribose moiety of guanosine to dihydroxyacetone phosphate and ethylene glycol. Although the metabolic route from guanosine to RuBP via R15P is similar to that of the pentose bisphosphate pathway in Thermococcales, the downstream route does not utilize Rubisco and is unique to halophilic archaea.
Topics: Ribulose-Bisphosphate Carboxylase; Ribose; Pentoses; Archaea; Guanosine; Phosphates
PubMed: 36434094
DOI: 10.1038/s42003-022-04247-2 -
Applied Microbiology and Biotechnology Apr 2007Production of bioethanol from forest and agricultural products requires a fermenting organism that converts all types of sugars in the raw material to ethanol in high... (Review)
Review
Production of bioethanol from forest and agricultural products requires a fermenting organism that converts all types of sugars in the raw material to ethanol in high yield and with a high rate. This review summarizes recent research aiming at developing industrial strains of Saccharomyces cerevisiae with the ability to ferment all lignocellulose-derived sugars. The properties required from the industrial yeast strains are discussed in relation to four benchmarks: (1) process water economy, (2) inhibitor tolerance, (3) ethanol yield, and (4) specific ethanol productivity. Of particular importance is the tolerance of the fermenting organism to fermentation inhibitors formed during fractionation/pretreatment and hydrolysis of the raw material, which necessitates the use of robust industrial strain background. While numerous metabolic engineering strategies have been developed in laboratory yeast strains, only a few approaches have been realized in industrial strains. The fermentation performance of the existing industrial pentose-fermenting S. cerevisiae strains in lignocellulose hydrolysate is reviewed. Ethanol yields of more than 0.4 g ethanol/g sugar have been achieved with several xylose-fermenting industrial strains such as TMB 3400, TMB 3006, and 424A(LNF-ST), carrying the heterologous xylose utilization pathway consisting of xylose reductase and xylitol dehydrogenase, which demonstrates the potential of pentose fermentation in improving lignocellulosic ethanol production.
Topics: Fermentation; Forecasting; Industrial Microbiology; Pentoses; Saccharomyces cerevisiae
PubMed: 17294186
DOI: 10.1007/s00253-006-0827-2 -
Microbiological Research Nov 2023Lignocellulosic biomass, consisting of homo- and heteropolymeric sugars, acts as a substrate for the generation of valuable biochemicals and biomaterials. The readily... (Review)
Review
Lignocellulosic biomass, consisting of homo- and heteropolymeric sugars, acts as a substrate for the generation of valuable biochemicals and biomaterials. The readily available hexoses are easily utilized by microbes due to the presence of transporters and native metabolic pathways. But, utilization of pentose sugar viz., xylose and arabinose are still challenging due to several reasons including (i) the absence of the particular native pathways and transporters, (ii) the presence of inhibitors, and (iii) lower uptake of pentose sugars. These challenges can be overcome by manipulating metabolic pathways/glycosidic enzymes cascade by using genetic engineering tools involving inverse-metabolic engineering, ex-vivo isomerization, Adaptive Laboratory Evolution, Directed Metabolic Engineering, etc. Metabolic engineering of bacteria and fungi for the utilization of pentose sugars for bioethanol production is the focus area of research in the current decade. This review outlines current approaches to biofuel development and strategies involved in the metabolic engineering of different microbes that can uptake pentose for bioethanol production.
Topics: Pentoses; Sugars; Metabolic Engineering; Biomass; Membrane Transport Proteins
PubMed: 37625339
DOI: 10.1016/j.micres.2023.127478 -
Environmental Microbiology Feb 2023The Pseudomonas putida group in the Gammaproteobacteria has been intensively studied for bioremediation and plant growth promotion. Members of this group have recently...
The Pseudomonas putida group in the Gammaproteobacteria has been intensively studied for bioremediation and plant growth promotion. Members of this group have recently emerged as promising hosts to convert intermediates derived from plant biomass to biofuels and biochemicals. However, most strains of P. putida cannot metabolize pentose sugars derived from hemicellulose. Here, we describe three isolates that provide a broader view of the pentose sugar catabolism in the P. putida group. One of these isolates clusters with the well-characterized P. alloputida KT2440 (Strain BP6); the second isolate clustered with plant growth-promoting strain P. putida W619 (Strain M2), while the third isolate represents a new species in the group (Strain BP8). Each of these isolates possessed homologous genes for oxidative xylose catabolism (xylDXA) and a potential xylonate transporter. Strain M2 grew on arabinose and had genes for oxidative arabinose catabolism (araDXA). A CRISPR interference (CRISPRi) system was developed for strain M2 and identified conditionally essential genes for xylose growth. A glucose dehydrogenase was found to be responsible for initial oxidation of xylose and arabinose in strain M2. These isolates have illuminated inherent diversity in pentose catabolism in the P. putida group and may provide alternative hosts for biomass conversion.
Topics: Pentoses; Xylose; Arabinose; Pseudomonas putida; Oxidative Stress
PubMed: 36465038
DOI: 10.1111/1462-2920.16296 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Oct 2018One of the requirements for increasing the economic profitability on the large-scale production of second-generation ethanol and other bio-chemicals using lignocellulose... (Review)
Review
One of the requirements for increasing the economic profitability on the large-scale production of second-generation ethanol and other bio-chemicals using lignocellulose biomass as raw materials is efficient hexose and pentose utilization. Saccharomyces cerevisiae, the traditional ethanol producer, is an attractive chassis cell due to its robustness towards harsh environmental conditions and inherent advantages. But S. cerevisiae cannot utilize pentose. The precision construction of suitable strains for second-generation bio-ethanol production has been taken for more than three decades based on the principle of metabolic engineering and synthetic biology. The resulting strains have improved significantly co-fermentation of glucose and xylose. Recently, much attentions have been focused on sugar transport, which is one of the limiting but formerly ignored step for ethanol production from both glucose and xylose, to get the desired state that different sugars could efficiently delivered by their individual specific transporters. In this paper, the progress on sugar transporters of S. cerevisiae was reviewed, and the research status of xylose and/or L-arabinose metabolic engineering in S. cerevisiae were also presented.
Topics: Arabinose; Biological Transport; Biomass; Ethanol; Fermentation; Glucose; Industrial Microbiology; Lignin; Metabolic Engineering; Monosaccharide Transport Proteins; Pentoses; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Xylose
PubMed: 30394022
DOI: 10.13345/j.cjb.180031