Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum
Marco A. van den Berg,Richard Albang,Kaj Albermann,Jonathan H. Badger,Jean-Marc Daran,Arnold J. M. Driessen,Carlos García-Estrada,Natalie D. Fedorova,Diana M. Harris,Wilbert H. M. Heijne,Vinita Joardar,Jan A.K.W. Kiel,Andriy Kovalchuk,Juan F. Martín,William C. Nierman,William C. Nierman,Jeroen G. Nijland,Jack T. Pronk,Johannes Andries Roubos,Ida J. van der Klei,Noël Nicolaas Maria Elisabeth Van Peij,Marten Veenhuis,Hans von Döhren,Christian Wagner,Jennifer R. Wortman,Roel A. L. Bovenberg +25 more
Reads0
Chats0
TLDR
Genes predicted to encode transporters were strongly overrepresented among the genes transcriptionally upregulated under conditions that stimulate penicillinG production, illustrating potential for future genomics-driven metabolic engineering.Abstract:
Industrial penicillin production with the filamentous fungus Penicillium chrysogenum is based on an unprecedented effort in microbial strain improvement. To gain more insight into penicillin synthesis, we sequenced the 32.19 Mb genome of P. chrysogenum Wisconsin54-1255 and identified numerous genes responsible for key steps in penicillin production. DNA microarrays were used to compare the transcriptomes of the sequenced strain and a penicillinG high-producing strain, grown in the presence and absence of the side-chain precursor phenylacetic acid. Transcription of genes involved in biosynthesis of valine, cysteine and alpha-aminoadipic acid-precursors for penicillin biosynthesis-as well as of genes encoding microbody proteins, was increased in the high-producing strain. Some gene products were shown to be directly controlling beta-lactam output. Many key cellular transport processes involving penicillins and intermediates remain to be characterized at the molecular level. Genes predicted to encode transporters were strongly overrepresented among the genes transcriptionally upregulated under conditions that stimulate penicillinG production, illustrating potential for future genomics-driven metabolic engineering.read more
Citations
More filters
Journal ArticleDOI
Plant and microbial strategies to improve the phosphorus efficiency of agriculture
Alan Richardson,Alan Richardson,Jonathan P. Lynch,Peter R. Ryan,Emmanuel Delhaize,F. Andrew Smith,Sally E. Smith,Paul R. Harvey,Megan H. Ryan,Erik J. Veneklaas,Hans Lambers,Astrid Oberson,Richard A. Culvenor,Richard J. Simpson,Richard J. Simpson +14 more
TL;DR: Evidence that more P-efficient plants can be developed by modifying root growth and architecture, through manipulation of root exudates or by managing plant-microbial associations such as arbuscular mycorrhizal fungi and microbial inoculants is critically reviewed.
Journal ArticleDOI
Fungal enzyme sets for plant polysaccharide degradation
TL;DR: This mini-review will discuss the enzymes needed for complete degradation of plant polysaccharides and will give an overview of the latest developments concerning fungal carbohydrate-active enzymes and their corresponding families.
Journal ArticleDOI
Enzymatic hydrolysis of cellulosic biomass
TL;DR: This review highlights literature on the impact of key substrate and enzyme features that influence performance to better understand fundamental strategies to advance enzymatic hydrolysis of cellulosic biomass for biological conversion to fuels and chemicals.
Journal ArticleDOI
Phylogeny of Penicillium and the segregation of Trichocomaceae into three families
Jos Houbraken,Robert A. Samson +1 more
TL;DR: The relationship of Penicillium to other genera of Trichocomaceae is investigated and a new classification system including both anamorph and teleomorph species is proposed and these 25 clades are treated here as sections.
Journal ArticleDOI
The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum
TL;DR: The RAVEN Toolbox workflow was applied in order to reconstruct a genome-scale metabolic model for the important microbial cell factory Penicillium chrysogenum Wisconsin54-1255, and was then used to study the roles of ATP and NADPH in the biosynthesis of Penicillin, and to identify potential metabolic engineering targets for maximization of penicillin production.
References
More filters
Book
Molecular Cloning: A Laboratory Manual
TL;DR: Molecular Cloning has served as the foundation of technical expertise in labs worldwide for 30 years as mentioned in this paper and has been so popular, or so influential, that no other manual has been more widely used and influential.
Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Some methods for classification and analysis of multivariate observations
TL;DR: The k-means algorithm as mentioned in this paper partitions an N-dimensional population into k sets on the basis of a sample, which is a generalization of the ordinary sample mean, and it is shown to give partitions which are reasonably efficient in the sense of within-class variance.
Book
Molecular Evolutionary Genetics
TL;DR: Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.
Related Papers (5)
Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88
Herman Jan Pel,Johannes H. de Winde,Johannes H. de Winde,David B. Archer,Paul S. Dyer,Gerald Hofmann,Peter J. Schaap,Geoffrey Turner,Ronald P. de Vries,Richard Albang,Kaj Albermann,Mikael Rørdam Andersen,Jannick Dyrløv Bendtsen,Jacques A.E. Benen,Marco A. van den Berg,Stefaan Breestraat,Mark X. Caddick,Roland Contreras,Michael Cornell,Pedro M. Coutinho,Etienne Danchin,Alfons J. M. Debets,Peter J. T. Dekker,Piet W.M. van Dijck,Alard Van Dijk,Lubbert Dijkhuizen,Arnold J. M. Driessen,Christophe d'Enfert,Steven Geysens,Coenie Goosen,Gert S.P. Groot,Piet W. J. de Groot,Thomas Guillemette,Bernard Henrissat,Marga Herweijer,Johannes Petrus Theodorus Wilhelmus Van Den Hombergh,Cees A. M. J. J. van den Hondel,René T. J. M. van der Heijden,Rachel M. van der Kaaij,Frans M. Klis,Harrie J. Kools,Christian P. Kubicek,Patricia Ann van Kuyk,Jürgen Lauber,Xin Lu,Marc J. E. C. van der Maarel,Rogier Meulenberg,Hildegard Henna Menke,Martin Mortimer,Jens Nielsen,Stephen G. Oliver,Maurien M.A. Olsthoorn,K. Pal,K. Pal,Noël Nicolaas Maria Elisabeth Van Peij,Arthur F. J. Ram,Ursula Rinas,Johannes Andries Roubos,Cornelis Maria Jacobus Sagt,Monika Schmoll,Jibin Sun,David W. Ussery,János Varga,Wouter Vervecken,Peter J.J. Van De Vondervoort,Holger Wedler,Han A. B. Wösten,An-Ping Zeng,Albert J. J. van Ooyen,Jaap Visser,Hein Stam +70 more
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
James E. Galagan,Sarah E. Calvo,Christina A. Cuomo,Li-Jun Ma,Jennifer R. Wortman,Serafim Batzoglou,Su-In Lee,Meray Baştürkmen,Christina C. Spevak,John Clutterbuck,Vladimir V. Kapitonov,Jerzy Jurka,Claudio Scazzocchio,Mark L. Farman,Jonathan Butler,Seth Purcell,Steve Harris,Gerhard H. Braus,Oliver W. Draht,Silke Busch,Christophe d'Enfert,Christiane Bouchier,Gustavo H. Goldman,Deborah Bell-Pedersen,Sam Griffiths-Jones,John H. Doonan,Jae-Hyuk Yu,Kay Vienken,Arnab Pain,Michael Freitag,Eric U. Selker,David B. Archer,Miguel A. Peñalva,Berl R. Oakley,Michelle Momany,Toshihiro Tanaka,Toshitaka Kumagai,Kiyoshi Asai,Masayuki Machida,William C. Nierman,David W. Denning,Mark X. Caddick,Michael J. Hynes,Mathieu Paoletti,Reinhard Fischer,Reinhard Fischer,Bruce L. Miller,Paul S. Dyer,Matthew S. Sachs,Stephen A. Osmani,Bruce W. Birren +50 more
Genome sequencing and analysis of Aspergillus oryzae
Masayuki Machida,Kiyoshi Asai,Motoaki Sano,Toshihiro Tanaka,Toshitaka Kumagai,Goro Terai,Goro Terai,Ken Ichi Kusumoto,Toshihide Arima,Osamu Akita,Yutaka Kashiwagi,Keietsu Abe,Katsuya Gomi,Hiroyuki Horiuchi,Katsuhiko Kitamoto,Tetsuo Kobayashi,Michio Takeuchi,David W. Denning,James E. Galagan,William C. Nierman,Jiujiang Yu,David B. Archer,Joan W. Bennett,Deepak Bhatnagar,Thomas E. Cleveland,Natalie D. Fedorova,Osamu Gotoh,Hiroshi Horikawa,Akira Hosoyama,Masayuki Ichinomiya,Rie Igarashi,Kazuhiro Iwashita,Praveen R. Juvvadi,Masashi Kato,Yumiko Kato,Taishin Kin,Akira Kokubun,Hiroshi Maeda,Noriko Maeyama,Jun-ichi Maruyama,Hideki Nagasaki,Tasuku Nakajima,Ken Oda,Kinya Okada,Ian T. Paulsen,Kazutoshi Sakamoto,Toshihiko Sawano,Mikio Takahashi,Kumiko Takase,Yasunobu Terabayashi,Jennifer R. Wortman,Osamu Yamada,Youhei Yamagata,Hideharu Anazawa,Yoji Hata,Yoshinao Koide,Takashi Komori,Yasuji Koyama,Toshitaka Minetoki,Sivasundaram Suharnan,Akimitsu Tanaka,Katsumi Isono,Satoru Kuhara,Naotake Ogasawara,Hisashi Kikuchi +64 more
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus
William C. Nierman,William C. Nierman,Arnab Pain,Michael J. Anderson,Jennifer R. Wortman,Jennifer R. Wortman,H. Stanley Kim,H. Stanley Kim,Javier Arroyo,Matthew Berriman,Keietsu Abe,David B. Archer,Clara Bermejo,Joan W. Bennett,Paul Bowyer,Dan Chen,Dan Chen,Matthew Collins,Richard Coulsen,Robert L. Davies,Paul S. Dyer,Mark L. Farman,Nadia Fedorova,Nadia Fedorova,Natalie D. Fedorova,Natalie D. Fedorova,T. Feldblyum,T. Feldblyum,Reinhard Fischer,Nigel Fosker,Audrey Fraser,José Luis García,María Josefa Marcos García,Ariette Goble,Gustavo H. Goldman,Katsuya Gomi,Sam Griffith-Jones,R. Gwilliam,Brian J. Haas,Brian J. Haas,Hubertus Haas,David Harris,H. Horiuchi,Jiaqi Huang,Jiaqi Huang,Sean Humphray,Javier Jiménez,Nancy P. Keller,H. Khouri,H. Khouri,Katsuhiko Kitamoto,Tetsuo Kobayashi,Sven Konzack,Resham Kulkarni,Resham Kulkarni,Toshitaka Kumagai,Anne Lafton,Jean-Paul Latgé,Weixi Li,Angela Lord,Charles Lu,Charles Lu,William H. Majoros,William H. Majoros,Gregory S. May,Bruce L. Miller,Yasmin Ali Mohamoud,Yasmin Ali Mohamoud,María Molina,Michel Monod,Isabelle Mouyna,Stephanie Mulligan,Stephanie Mulligan,Lee Murphy,Susan O'Neil,Ian T. Paulsen,Ian T. Paulsen,Miguel A. Peñalva,Mihaela Pertea,Mihaela Pertea,Claire Price,Bethan L. Pritchard,Michael A. Quail,Ester Rabbinowitsch,Neil Rawlins,Marie Adele Rajandream,Utz Reichard,Hubert Renauld,Geoffrey D. Robson,Santiago Rodríguez de Córdoba,José Manuel Rodríguez-Peña,Catherine M. Ronning,Catherine M. Ronning,Simon Rutter,Steven L. Salzberg,Steven L. Salzberg,Miguel del Nogal Sánchez,Juan C. Sánchez-Ferrero,David L. Saunders,Kathy Seeger,Rob Squares,S. Squares,Michio Takeuchi,Fredj Tekaia,Geoffrey Turner,Carlos R. Vázquez de Aldana,J. Weidman,J. Weidman,Owen White,Owen White,John Woodward,Jae-Hyuk Yu,Claire M. Fraser,Claire M. Fraser,James E. Galagan,Kiyoshi Asai,Masayuki Machida,Neil Hall,Neil Hall,Bart Barrell,David W. Denning +120 more