Article
Biochemistry & Molecular Biology
Pietro Boccaletto, Filip Stefaniak, Angana Ray, Andrea Cappannini, Sunandan Mukherjee, Elzbieta Purta, Malgorzata Kurkowska, Niloofar Shirvanizadeh, Eliana Destefanis, Paula Groza, Gulben Avsar, Antonia Romitelli, Pinar Pir, Erik Dassi, Silvestro G. Conticello, Francesca Aguilo, Janusz M. Bujnicki
Summary: MODOMICS database, established since 2006, has evolved from containing basic chemical structures of modified ribonucleosides to a comprehensive resource with new functionalities such as a catalog of RNA modifications linked to human diseases. The database, which is extensively linked to RCSB Protein Data Bank, provides users with an enhanced tool for research on RNA modification.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Morgan Price, Adam O. Deutschbauer, Adam Arkin
Summary: To discover novel catabolic enzymes and transporters, the researchers combined high-throughput genetic data from 29 bacteria with an automated tool. They used GapMind to annotate the uptake and catabolism of compounds in bacterial and archaeal genomes, and systematically examined the gaps in predicted pathways. They identified new pathways or enzymes for the utilization of various compounds and annotated numerous enzymes and transporters.
Article
Biochemistry & Molecular Biology
Xiang Li, Mi Li, Yunqiao Pu, Arthur J. Ragauskas, Nishanth Tharayil, Jiale Huang, Yi Zheng
Summary: This paper investigated a novel high biomass strain of marine protist Thraustochytrium striatum for lignin valorization to lipids and carotenoids. The strain demonstrated the ability to utilize various aromatic compounds and achieved optimal growth on 3,4-dihydroxybenzoic acid and 4-hydroxybenzoic acid. Adoption of fed-batch fermentation mode improved the degradation of carbon source and enhanced the production of cellular fatty acids and carotenoids.
PROCESS BIOCHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Alexandra M. Linz, Yanjun Ma, Jose M. Perez, Kevin S. Myers, Wayne S. Kontur, Daniel R. Noguera, Timothy J. Donohue
Summary: This study demonstrates the ability of Novosphingobium aromaticivorans to metabolize specific chemical compounds derived from lignin depolymerization, expanding its potential range of substrates. The findings also suggest opportunities for producing industrial chemicals from the heterogenous components of lignin using engineered microbes and enzymes.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Environmental Sciences
Leizhen Rao, Decheng Gu, Xingjia Xiang, Jun Zeng, Yucheng Wu, Xiangui Lin, Peter Christie
Summary: Lignin, a complex biopolymer, can enhance the degradation of soil pollutants, but the contribution of its constituents to this process is not well understood. This study found that vanillate and p-hydroxybenzoate significantly promoted the mineralization of polycyclic aromatic hydrocarbons (PAHs), while methanol had no effect. The different constituents of lignin also had different effects on the soil bacterial community. Overall, lignin had extensive impacts on bacterial diversity, composition, and the fate of PAHs.
ENVIRONMENTAL POLLUTION
(2023)
Review
Chemistry, Multidisciplinary
Alexander J. D. Snow, Laura Burchill, Mahima Sharma, Gideon J. Davies, Spencer J. Williams
Summary: Sulfoquinovose (SQ) is a derivative of glucose produced by photosynthetic organisms, and its degradation plays a key role in the global sulfur and carbon biogeochemical cycles. Bacteria degrade SQ through two main pathways: one involves breaking down the 6-carbon skeleton of SQ into two fragments, while the other involves complete metabolism through desulfonylation to release sulfite and glucose. Discovery of sulfoglycolytic pathways has revealed novel enzymes and binding proteins, shedding light on how the sulfonate group is recognized and its relationship to glycolysis pathways.
CHEMICAL SOCIETY REVIEWS
(2021)
Article
Agricultural Engineering
Misa Mojca Cajnko, Jost Oblak, Miha Grilc, Blaz Likozar
Summary: Enzymes play a crucial role in lignin valorization, with different enzymes involved in various elementary reaction mechanisms. Degradation of lignin depends on enzyme activity and the interaction with proteins in ways that target specific covalent bonds in lignin. Various factors influence enzymatic activity, which must be taken into consideration for optimal functionality and synthesis yields.
BIORESOURCE TECHNOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Ali Mohamed Elyamine, Jie Kan, Shanshan Meng, Peng Tao, Hui Wang, Zhong Hu
Summary: Microbial biodegradation is an effective technology for remediating and controlling pollution by polycyclic aromatic hydrocarbons, involving aerobic and anaerobic degradation pathways by various bacteria and fungi. Understanding the key actors, steps, and mechanisms of pyrene degradation is crucial for addressing PAH pollution. Further research on anaerobic pyrene degradation is recommended to elucidate the degradation pathway and enhance biodegradation efficiency through microbial consortia.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Alexandra M. Linz, Yanjun Ma, Samuel Scholz, Daniel R. Noguera, Timothy J. Donohue
Summary: Lignin is a renewable source of aromatics and precursors for organic chemicals. The heterogeneous nature of lignin makes its conversion to chemicals challenging. By using the genome-scale metabolic model iNovo479, we can predict the product yields of microbial conversion of lignin aromatics into valuable chemicals and optimize strain engineering.
Article
Microbiology
Wilfried Poirier, Kevin Ravenel, Jean-Philippe Bouchara, Sandrine Giraud
Summary: The study found that the adaptation mechanisms of Scedosporium species to their environment involve specific catabolism pathways, particularly the lower funneling pathways. These pathways open the aromatic ring of molecules through dioxygenases, leading to the tricarboxylic acid cycle. When cultivated in the presence of lignin or gentisic acid as the sole carbon source, the genes of the gentisic acid cluster in Scedosporium species were markedly overexpressed, indicating their involvement in Scedosporium adaptation to the environment.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Carlos del Cerro, Erika Erickson, Tao Dong, Allison R. Wong, Elizabeth K. Eder, Samuel O. Purvine, Hugh D. Mitchell, Karl K. Weitz, Lye Meng Markillie, Meagan C. Burnet, David W. Hoyt, Rosalie K. Chu, Jan-Fang Cheng, Kelsey J. Ramirez, Rui Katahira, Wei Xiong, Michael E. Himmel, Venkataramanan Subramanian, Jeffrey G. Linger, Davinia Salvachua
Summary: Research shows that two white-rot fungi can utilize lignin as a carbon source and funnel carbon from lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These insights into global carbon cycling and the foundation for a sustainable bioeconomy highlight the importance of simultaneous lignin depolymerization and bioconversion by white-rot fungi.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Oncology
Aoyu Fan, Yunyan Zhang, Jiangting Cheng, Yunpeng Li, Wei Chen
Summary: In this study, a prognostic model containing 13 genes was constructed to predict biochemical recurrence in prostate cancer patients. The study identified key pathways associated with patient prognosis and analyzed the characteristics of high-risk and low-risk groups. Additionally, two potential therapeutic targets were identified.
FRONTIERS IN ONCOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Zhi-Min Zhao, Xianzhi Meng, Manjula Senanayake, Sai Venkatesh Pingali, Yunqiao Pu, Mi Li, Litong Ma, Jifei Xu, Arthur J. Ragauskas
Summary: This study introduces a strategy to eliminate thermal sterilization, which significantly enhances the dispersion of lignin in aqueous fermentation media. This promotes lignin bioconversion efficiently.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2022)
Article
Chemistry, Multidisciplinary
Zhi-Min Zhao, Shuyang Zhang, Xianzhi Meng, Yunqiao Pu, Zhi-Hua Liu, William K. Ledford, S. Michael Kilbey, Bing-Zhi Li, Arthur J. Ragauskas
Summary: Alkali sterilization effectively enhances the dispersion and fermentation performance of lignin substrates, improving bioconversion efficiency. Changes in particle size and molecular structure of lignin after alkali sterilization, including the generation of more hydrophilic carboxyl groups, reduction in molecular weight, and narrowing molar-mass dispersity, promote Rhodococcus opacus PD630 cell growth and metabolism, leading to increased lignin degradation and lipid production.
Article
Biotechnology & Applied Microbiology
Fabia Weiland, Michael Kohlstedt, Christoph Wittmann
Summary: Lignin, an important structural component of plants, is considered as an under-utilized and promising feedstock due to its abundance and richness in aromatics. Microbes have evolved enzymes and pathways to break down lignin and metabolize its aromatic components. Systems metabolic engineering offers a sustainable approach to upgrade lignin into a variety of valuable products.
METABOLIC ENGINEERING
(2022)
Article
Biotechnology & Applied Microbiology
Javier Garcia-Hidalgo, Daniel P. Brink, Krithika Ravi, Catherine J. Paul, Gunnar Liden, Marie F. Gorwa-Grauslund
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Thales H. F. Costa, Adnan Kadic, Piotr Chylenski, Aniko Varnai, Oskar Bengtsson, Gunnar Liden, Vincent G. H. Eijsink, Svein Jarle Horn
BIOFUELS BIOPRODUCTS & BIOREFINING-BIOFPR
(2020)
Article
Biotechnology & Applied Microbiology
Adnan Kadic, Aniko Varnai, Vincent G. H. Eijsink, Svein Jarle Horn, Gunnar Liden
Summary: Biochemical conversion of lignocellulosic biomass to sugars is hindered by high saccharifying enzyme costs. LPMOs offer potential solutions, but overdosing H2O2 can lead to enzyme inactivation. In this study, real-time monitoring of oxidation-reduction potential and H2O2 concentration allowed for predicting LPMO inactivation during enzymatic saccharification, potentially improving overall yields.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
Article
Biotechnology & Applied Microbiology
Joana Campos, Jie Bao, Gunnar Liden
Summary: This study demonstrates that two modified strains efficiently utilize high mannose content in softwood hydrolysate to produce high-purity L and D-lactic acid. Despite lower mannose utilization rates compared to glucose, this research provides important insights for future production of chiral lactic acid from lignocellulosic feedstocks.
JOURNAL OF BIOTECHNOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Daniel P. Brink, Celina Borgstrom, Viktor C. Persson, Karen Ofuji Osiro, Marie F. Gorwa-Grauslund
Summary: Investigation on the signaling response of Saccharomyces cerevisiae to d-xylose and attempts to improve the response through signaling engineering.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Polymer Science
Roujin Ghaffari, Henrik Almqvist, Robin Nilsson, Gunnar Liden, Anette Larsson
Summary: This study investigated the diffusion of kraft lignin molecules through model cellulose membranes of varying pore sizes. The results showed that small pore sizes enable the diffusion of small molecules while hindering the transport of larger molecules or clusters. This study provides important insights into the mass transfer events in pulping processes.
Article
Biochemistry & Molecular Biology
Joana Campos, Lorenzo Garcia Tejada, Jie Bao, Gunnar Liden
Summary: The study focuses on the production of optically pure L-lactic acid (LA) from softwood hydrolysate with Pediococcus acidilactici TY112. It is found that the strain is capable of converting inhibitors and partly detoxifying the hydrolysate and synthetic media, indicating its potential for L-LA production.
PROCESS BIOCHEMISTRY
(2023)
Article
Genetics & Heredity
Friederike Mierke, Daniel P. Brink, Joakim Norbeck, Verena Siewers, Thomas Andlid
Summary: In this study, the oleaginous nature of P. hubeiensis was further characterized by evaluating its metabolism and gene expression responses during storage lipid formation conditions with glucose or xylose as a carbon source. The genome of P. hubeiensis BOT-O strain was sequenced, generating the first mRNA-supported genome annotation and identifying 6540 genes. The study revealed that BOT-O can efficiently utilize both glucose and xylose, with glucose being taken up faster during mixed cultivation. Nitrogen-starvation had a significant transcriptional effect on the expression of 1179 genes.
FUNGAL GENETICS AND BIOLOGY
(2023)
Article
Microbiology
Nikhil Seshagiri Rao, Ludwig Ermann Lundberg, Julia Tomasson, Cecilia Tullberg, Daniel P. Brink, Shuai Bai Palmkron, Ed W. J. van Niel, Sebastian Hakansson, Magnus Carlquist
Summary: The study investigated the effects of oxygen on Limosilactobacillus reuteri DSM 17938 during cultivation and the resulting properties of the freeze-dried probiotic product. It was found that low levels of oxygen did not influence the growth kinetics of the bacterium, but did affect the redox metabolism and production of acetate and ethanol. Cells cultivated in the presence of oxygen showed higher survival rates, increased unsaturated fatty acid content, improved bile tolerance, and higher 5' nucleotidase activity. However, they exhibited lower tolerance to acidic conditions compared to bacteria grown under complete anaerobic conditions. Overall, controlled oxygen supply during production can optimize the probiotic activity of L. reuteri DSM 17938.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Daniel P. Brink, Elin M. Larsson, Javier Garcia-Hidalgo, Helga Helgadottir, Marie F. Gorwa-Grauslund
Summary: Two bacterial strains (S1 and S4) capable of using syringol as the only carbon source were isolated from compost and sequenced using the Illumina platform. The final assemblies of S1 and S4 genomes were found to have 4.2 Mbp, 63% GC, and 3,912 genes, and 6.2 Mbp, 64% GC, and 5,503 genes, respectively.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Biotechnology & Applied Microbiology
Daniel P. Brink, Friederike Mierke, Joakim Norbeck, Verena Siewers, Thomas Andlid
Summary: In this study, six new R. toruloides promoters that were either upregulated or downregulated under nitrogen-starvation were identified. These promoters are expected to be particularly useful for future engineering strategies requiring specific regulation of target genes in accordance with nitrogen availability.
MICROBIAL CELL FACTORIES
(2023)
Article
Biotechnology & Applied Microbiology
Joao R. M. Almeida, Magnus Wiman, Dominik Heer, Daniel P. Brink, Uwe Sauer, Baerbel Hahn-Hagerdal, Gunnar Liden, Marie F. Gorwa-Grauslund
Summary: To evaluate the capability of Saccharomyces cerevisiae to adapt to lignocellulosic hydrolysates, the physiological effect of cultivating yeast in spruce hydrolysate was comprehensively studied. The yeast developed a rapid adaptive response to lignocellulosic hydrolysate, significantly improving its fermentation performance in subsequent experiments. The adaptive response involved the induction of NADPH-dependent aldehyde reductases and conversion of phenolic compounds.
FERMENTATION-BASEL
(2023)