Article
Biotechnology & Applied Microbiology
Katrin Wefelmeier, Birgitta E. Ebert, Lars M. Blank, Simone Schmitz
Summary: In this study, the influence of different promoters and terminators on gene expression in Ogataea polymorpha was characterized. It was found that these genetic elements not only affect the strength of gene expression, but also the timing of maximal expression. By varying the terminators, a significant difference in gene expression was achieved, and it was shown that this difference is due to the stabilization of mRNA. Additionally, it was found that different combinations of promoters and terminators or the expression of a different gene do not affect the performance of the genetic parts, allowing for flexible tuning of gene expression in O. polymorpha.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Katrin Wefelmeier, Simone Schmitz, Anna Maria Haut, Johannes Otten, Tobias Juelich, Lars Mathias Blank
Summary: This study explores the potential of using methanol as a substrate for lactate production by the methylotrophic yeast Ogataea polymorpha. It was found that the L-lactate dehydrogenase from Lactobacillus helveticus performed well in the yeast, and the lactate production of the engineered strain was further improved by methanol fed-batch experiments. The results demonstrate that Ogataea polymorpha is a suitable host organism for lactate production using methanol as a carbon source.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Review
Microbiology
Lukas Bernauer, Astrid Radkohl, Leonie Gabriela Katharina Lehmayer, Anita Emmerstorfer-Augustin
Summary: K. phaffii is an important model organism for studying eukaryotic molecular cell biology, with the intriguing property of being able to efficiently assimilate methanol. Research topics on this yeast range from studying methanol assimilation, peroxisome biogenesis and pexophagy to other cellular processes such as protein secretion, lipid biosynthesis and cell wall biogenesis. Comparing data obtained from K. phaffii with other yeasts can elucidate major differences and highlight its big potential in fundamental research.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biology
Binyang Deng, Yu Yue, Jun Yang, Mingjun Yang, Qiong Xing, Hang Peng, Fei Wang, Ming Li, Lixin Ma, Chao Zhai
Summary: In this study, highly glycosylated IsPETase enzyme was obtained by controlling the glycosylation modification of PETase in Pichia pastoris, improving the enzyme's specific activity and thermostability. The partially deglycosylated IsPETase still maintained high thermostability and could completely degrade PET flakes at 50 degrees C. This study provides a strategy to modulate the thermostable IsPETase through glycosylation engineering, promoting PET biodegradation.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Fidan Erden-Karaoglan, Mert Karaoglan
Summary: This study investigated the applicability of heterologous yeast promoters in Pichia pastoris, and found inducible and constitutive regulation modes as well as the optimal carbon sources for these promoters. The study also determined the DNA region with the highest activity for all promoters through promoter deletion analysis.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Microbiology
Jia Chang, Jinlong Bei, Qi Shao, Hemu Wang, Huan Fan, Tung On Yau, Wenjun Bu, Jishou Ruan, Dongsheng Wei, Shan Gao
Summary: The present study successfully assembled the full-length genome of O. polymorpha HU-11/CBS4732 using high-depth PacBio and Illumina data, and determined important genomic differences between HU-11/CBS4732 and NCYC495. The relationship between CBS4732, NCYC495, and DL-1 has been preliminarily revealed, and the findings provide new opportunities for understanding genome evolution in methylotrophic yeasts and for industrial applications of O. polymorpha strains.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Maria Carmela Bonaccorsi di Patti, Antimo Cutone, Zuzana Pakanova, Marek Nemcovic, Peter Barath, Giovanni Musci
Summary: Ceruloplasmin is crucial for iron metabolism in vertebrates, and the production of high-quality recombinant human ceruloplasmin represents a significant advancement. Further improvement in productivity and glycoengineering is necessary for potential therapeutic use in aceruloplasminemia patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Tianpeng Chen, Shimeng Wang, Huanqing Niu, Guanjia Yang, Sinan Wang, Yuqi Wang, Chaowei Zhou, Bin Yu, Pengpeng Yang, Wenjun Sun, Dong Liu, Hanjie Ying, Yong Chen
Summary: A biofilm-based fermentation system was constructed in P. pastoris by combining the surface display of beta-galactosidase and biofilm formation. The results showed a catalytic conversion rate of 50.3% for GOS with a maximum enzyme activity of 5125 U/g. This study provides a basis for developing biofilm-based surface display methods in P. pastoris.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Nai-Xin Lin, Rui-Zhen He, Yan Xu, Xiao-Wei Yu
Summary: The robust P. pastoris mutant demonstrates higher expression levels of not only lipase but also other heterogeneous proteins under methanol induction conditions. The mutant shows lower intracellular ROS levels compared to the WT. RNA-seq analysis revealed upregulation of key pathways related to antioxidant, MAPK pathway, ergosterol synthesis pathway, transcription factors, and the peroxisome pathway in the robust mutant, contributing to its enhanced oxidative stress tolerance and high heterologous protein expression efficiency.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
Article
Microbiology
Tingting Niu, Yi Cui, Xu Shan, Shuzhen Qin, Xuejie Zhou, Rui Wang, Alan Chang, Nan Ma, Jingjing Jing, Jianwei He
Summary: The study showed that coexpression of PDI can increase the extracellular levels of both wild-type cC and two mutants, preventing misfolding of unstable proteins or promoting the degradation of misfolded proteins. Transcriptomic analysis of P. pastoris cells expressing different stability exogenous proteins revealed significant changes in signaling pathways and cell components, providing valuable insights for improving heterologous protein expression efficiency.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Lina Heistinger, Juliane C. Dohm, Barbara G. Paes, Daniel Koizar, Christina Troyer, Oezge Ata, Teresa Steininger-Mairinger, Diethard Mattanovich
Summary: By characterizing 25 natural isolates from all seven described Komagataella species, this study identified strains with differences in tolerance to high pH, high temperature, and growth on xylose. The genotypic and phenotypic diversity within this genus provides a basis for utilizing neglected Komagataella strains with interesting characteristics and understanding genetic determinants for improved growth and stress tolerance.
MICROBIAL CELL FACTORIES
(2022)
Article
Biology
Alexander N. Malyavko, Olga A. Petrova, Maria Zvereva, Vladimir Polshakov, Olga A. Dontsova
Summary: This study reports the functional characterization of the Rif1 homologue from the methylotrophic thermotolerant budding yeast Hansenula polymorpha DL-1. The study reveals that Rif1 in H. polymorpha suppresses telomerase-dependent telomere elongation through direct DNA binding and association with the Ku heterodimer. It is also found that Rif1 binds Stn1 and promotes its accumulation at telomeres in H. polymorpha.
Article
Microbiology
Yasmin Nabilah Binti Mohd Fauzee, Yuki Yoshida, Yukio Kimata
Summary: In eukaryotic species, dysfunction of the endoplasmic reticulum (ER) triggers a cellular protective response called the unfolded protein response (UPR). This response is initiated by ER stress sensors, including Ire1, which splices and matures mRNA encoding the transcription factor Hac1. Through analyzing the methylotrophic yeast Pichia pastoris, researchers discovered a previously unknown function of Ire1. They found that Ire1 not only regulates UPR but also controls protein aggregation and the heat shock response, conferring heat stress resistance to the cells.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Pharmacology & Pharmacy
Yoshiki Eto, Narcis Saubi, Pau Ferrer, Joan Joseph-Munne
Summary: This study established a method for producing chimeric HPV-HIV L1P18 protein in Pichia pastoris, achieving VLPs with a purity of 96% using a combination of purification techniques. This work contributes towards the development of an alternative platform for production of a bivalent vaccine against HPV and HIV.
Article
Biochemistry & Molecular Biology
Mirelle Flores-Villegas, Corinna Rebnegger, Viktoria Kowarz, Roland Prielhofer, Diethard Mattanovich, Brigitte Gasser
Summary: The promoter of the high-affinity glucose transporter Gth1 (PGTH1) was improved through random and rational engineering, resulting in stronger induction in glucose-limitation and enabling methanol-free production processes. Single point mutations and key promoter segments were identified, leading to a library of novel promoter variants with significantly higher activity. The study also discovered nucleotide positions and corresponding TFBS that distinguish between glycerol- and glucose-mediated repression of the native promoter.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Anjan Venkatesh, Anthony L. Murray, Aisling Y. Coughlan, Kenneth H. Wolfe
Summary: A study on yeast species in the genus Torulaspora found that some strains have larger GAL clusters with additional genes, indicating strong natural selection on the GAL pathway in this genus.
Article
Microbiology
Adam Ryan, Eoin O. Cinneide, Sean A. Bergin, Ghozlan Alhajeri, Hawraa Almotawaa, Isabelle Daly, Sophia Heneghan, Kellie Horan, Roslyn Kavanagh, Christopher Keane, Aaron Martin, Ada McDonagh, Julia O'Leary, Matthieu Osborne, Emma Watson, Kevin P. Byrne, Kenneth H. Wolfe, Geraldine Butler
Summary: Candida sanyaensis is a CUG-Ser1 clade yeast associated with soil, with a diploid and hybrid genome showing approximately 97% identity between haplotypes. The haploid genome size is approximately 15.4 Mb.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Review
Microbiology
Kenneth H. Wolfe, Geraldine Butler
Summary: This review focuses on recent progress in understanding the origins and evolution of mating-type switching systems in budding yeasts, highlighting the multiple independent occurrences and convergent evolution of these mechanisms, as well as the diversity of self-fertilization mechanisms.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2022)
Article
Multidisciplinary Sciences
Maria Paula Rueda-Mejia, Lukas Nageli, Stefanie Lutz, Raul A. Ortiz-Merino, Daniel Frei, Jurg E. Frey, Kenneth H. Wolfe, Christian H. Ahrens, Florian M. Freimoser
Summary: Cyberlindnera sargentensis strain SHA 17.2, isolated from a Swiss soil sample, shows strong antagonistic activity against various plant pathogenic fungi and demonstrates high competitiveness against other yeasts in soil. The sequencing and annotation of its genome provide a valuable resource for understanding the mode of action of C. sargentensis against fungal plant pathogens and for comparative genomics analysis of yeast genomes.
Article
Microbiology
Sean A. Bergin, Fang Zhao, Adam P. Ryan, Carolin A. Muller, Conrad A. Nieduszynski, Bing Zhai, Thierry Rolling, Tobias M. Hohl, Florent Morio, Jillian Scully, Kenneth H. Wolfe, Geraldine Butler
Summary: We analyzed the genomes of 170 C. parapsilosis isolates and identified multiple copy number variations (CNVs). We found that the increased copy number of the RTA3 gene is associated with resistance to the drug miltefosine. Additionally, we discovered that mutations in flippase genes can also contribute to resistance.
Article
Microbiology
Aida Don, Kevin P. Byrne, Fouz Alqaderi, Alexandra Mazhova, Ben O'Leary Chaney, Sarah Redmond, Stephen Allen, Jiaran Gao, Eoin O. Cinneide, Sean A. Bergin, Conor Hession, Kenneth H. Wolfe, Geraldine Butler
Summary: In this study, the genome sequence of Blastobotrys aristata UCD613, isolated from soil in Dublin, Ireland, was presented. The genome is 13.3 Mb in size and was assembled into 4 chromosome-size scaffolds of >2.2 Mb, along with a mitochondrial genome scaffold.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Microbiology
Blessing Igharo, Kevin P. Byrne, Heytham Ghnewa, Ryan P. Davey, Athaliah Fubara, Julia Welc, Shafik Oubihi, Luke Moore, Cian Smith, Eoin O. Cinneide, Sean A. Bergin, Conor Hession, Kenneth H. Wolfe, Geraldine Butler
Summary: The genome sequence of Torulaspora quercuum isolate UCD657, a yeast first isolated in 2009, was presented in this study. The genome is 10.4 Mb in size and was assembled into 8 chromosome-sized scaffolds and a mitochondrial genome scaffold.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Biochemistry & Molecular Biology
Benjamin Offei, Stephanie Braun-Galleani, Anjan Venkatesh, William T. Casey, Kevin E. O'Connor, Kevin P. Byrne, Kenneth H. Wolfe
Summary: By crossing different isolates of K. phaffii and sequencing their genomes, this study identified two QTLs in different genes that affect the secretion of heterologous protein beta-glucosidase. This demonstrates the importance of QTL analysis in studying biotechnological traits in nonconventional yeasts.
Article
Genetics & Heredity
Letal Salzberg, Alexandre A. R. Martos, Lisa Lombardi, Lars S. Jermiin, Alfonso Blanco, Kevin P. Byrne, Kenneth H. Wolfe
Summary: We investigated the only known inversion polymorphism in S. cerevisiae, which affects a 24-kb 'flip/flop' region near the centromere of chromosome XIV. The inversion polymorphism is at least 17 million years old and is conserved across the genus Saccharomyces. The REF and INV isomers are not ancient alleles but are continually being re-created by re-inversion of the region within each species.
Article
Biotechnology & Applied Microbiology
Sean A. Bergin, Stephen Allen, Conor Hession, Eoin O. Cinneide, Adam Ryan, Kevin P. Byrne, Tadhg O. Croinin, Kenneth H. Wolfe, Geraldine Butler
Summary: Lager brewing originated in 15th century Bavaria and is associated with cold weather brewing restrictions. Lager yeast, a hybrid of Saccharomyces cerevisiae and Saccharomyces eubayanus, is cold tolerant and is found only in industrial settings. Natural isolates of S. eubayanus were first discovered in Patagonia and have since been found in China, Tibet, New Zealand, and North America, but not in Europe. This study describes the first European strains of S. eubayanus isolated from a wooded area on a university campus in Dublin, Ireland, and provides genome analysis of these isolates.
FEMS YEAST RESEARCH
(2022)