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Arasti S, Tabaghi P, Tabatabaee Y, Mirarab S. Branch Length Transforms using Optimal Tree Metric Matching. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.13.566962. [PMID: 38746464 PMCID: PMC11092445 DOI: 10.1101/2023.11.13.566962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The abundant discordance between evolutionary relationships across the genome has rekindled interest in ways of comparing and averaging trees on a shared leaf set. However, most attempts at reconciling trees have focused on tree topology, producing metrics for comparing topologies and methods for computing median tree topologies. Using branch lengths, however, has been more elusive, due to several challenges. Species tree branch lengths can be measured in many units, often different from gene trees. Moreover, rates of evolution change across the genome, the species tree, and specific branches of gene trees. These factors compound the stochasticity of coalescence times. Thus, branch lengths are highly heterogeneous across both the genome and the tree. For many downstream applications in phylogenomic analyses, branch lengths are as important as the topology, and yet, existing tools to compare and combine weighted trees are limited. In this paper, we make progress on the question of mapping one tree to another, incorporating both topology and branch length. We define a series of computational problems to formalize finding the best transformation of one tree to another while maintaining its topology and other constraints. We show that all these problems can be solved in quadratic time and memory using a linear algebraic formulation coupled with dynamic programming preprocessing. Our formulations lead to convex optimization problems, with efficient and theoretically optimal solutions. While many applications can be imagined for this framework, we apply it to measure species tree branch lengths in the unit of the expected number of substitutions per site while allowing divergence from ultrametricity across the tree. In these applications, our method matches or surpasses other methods designed directly for solving those problems. Thus, our approach provides a versatile toolkit that finds applications in similar evolutionary questions. Code availability The software is available at https://github.com/shayesteh99/TCMM.git . Data availability Data are available on Github https://github.com/shayesteh99/TCMM-Data.git .
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Barreiro C, Albillos SM, García-Estrada C. Penicillium chrysogenum: Beyond the penicillin. ADVANCES IN APPLIED MICROBIOLOGY 2024; 127:143-221. [PMID: 38763527 DOI: 10.1016/bs.aambs.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
Almost one century after the Sir Alexander Fleming's fortuitous discovery of penicillin and the identification of the fungal producer as Penicillium notatum, later Penicillium chrysogenum (currently reidentified as Penicillium rubens), the molecular mechanisms behind the massive production of penicillin titers by industrial strains could be considered almost fully characterized. However, this filamentous fungus is not only circumscribed to penicillin, and instead, it seems to be full of surprises, thereby producing important metabolites and providing expanded biotechnological applications. This review, in addition to summarizing the classical role of P. chrysogenum as penicillin producer, highlights its ability to generate an array of additional bioactive secondary metabolites and enzymes, together with the use of this microorganism in relevant biotechnological processes, such as bioremediation, biocontrol, production of bioactive nanoparticles and compounds with pharmaceutical interest, revalorization of agricultural and food-derived wastes or the enhancement of food industrial processes and the agricultural production.
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Affiliation(s)
- Carlos Barreiro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Facultad de Veterinaria, Universidad de León, León, Spain; Instituto de Biología Molecular, Genómica y Proteómica (INBIOMIC), Universidad de León, León, Spain.
| | - Silvia M Albillos
- Área de Bioquímica y Biología Molecular, Departamento de Biotecnología y Ciencia de los Alimentos, Facultad de Ciencias, Universidad de Burgos, Burgos, Spain
| | - Carlos García-Estrada
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, León, Spain; Instituto de Biomedicina (IBIOMED), Universidad de León, León, Spain
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Sawant AM, Navale VD, Vamkudoth KR. Genome sequencing and analysis of penicillin V producing Penicillium rubens strain BIONCL P45 isolated from India. Int Microbiol 2024:10.1007/s10123-024-00491-0. [PMID: 38388812 DOI: 10.1007/s10123-024-00491-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/03/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
BACKGROUND A filamentous fungus Penicillium rubens is widely recognized for producing industrially important antibiotic, penicillin at industrial scale. OBJECTIVE To better comprehend, the genetic blueprint of the wild-type P. rubens was isolated from India to identify the genetic/biosynthetic pathways for phenoxymethylpenicillin (penicillin V, PenV) and other secondary metabolites. METHOD Genomic DNA (gDNA) was isolated, and library was prepared as per Illumina platform. Whole genome sequencing (WGS) was performed according to Illumina NovoSeq platform. Further, SOAPdenovo was used to assemble the short reads validated by Bowtie-2 and SAMtools packages. Glimmer and GeneMark were used to dig out total genes in genome. Functional annotation of predicted proteins was performed by NCBI non-redundant (NR), UniProt, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) databases. Moreover, secretome analysis was performed by SignalP 4.1 and TargetP v1.1 and carbohydrate-active enzymes (CAZymes) and protease families by CAZy database. Comparative genome analysis was performed by Mauve 2.4.0. software to find genomic correlation between P. rubens BIONCL P45 and Penicillium chrysogenum Wisconsin 54-1255; also phylogeny was prepared with known penicillin producing strains by ParSNP tool. RESULTS Penicillium rubens BIONCL P45 strain was isolated from India and is producing excess PenV. The 31.09 Mb genome was assembled with 95.6% coverage of the reference genome P. chrysogenum Wis 54-1255 with 10687 protein coding genes, 3502 genes had homologs in NR, UniProt, KEGG, and GO databases. Additionally, 358 CAZymes and 911 transporter coding genes were found in genome. Genome contains complete pathways for penicillin, homogentisate pathway of phenyl acetic acid (PAA) catabolism, Andrastin A, Sorbicillin, Roquefortine C, and Meleagrin. Comparative genome analysis of BIONCL P45 and Wis 54-1255 revealed 99.89% coverage with 2952 common KEGG orthologous protein-coding genes. Phylogenetic analysis revealed that BIONCL P45 was clustered with Fleming's original isolate P. rubens IMI 15378. CONCLUSION This genome can be a helpful resource for further research in developing fermentation processes and strain engineering approaches for high titer penicillin production.
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Affiliation(s)
- Amol M Sawant
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, Maharashtra, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vishwambar D Navale
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, Maharashtra, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Koteswara Rao Vamkudoth
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, Maharashtra, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Liu X, Wang X, Zhou F, Xue Y, Liu C. Genomic insights into Penicillium chrysogenum adaptation to subseafloor sedimentary environments. BMC Genomics 2024; 25:4. [PMID: 38166640 PMCID: PMC10759354 DOI: 10.1186/s12864-023-09921-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Penicillium chrysogenum is a filamentous fungal species with diverse habitats, yet little is known about its genetics in adapting to extreme subseafloor sedimental environments. RESULTS Here, we report the discovery of P. chrysogenum strain 28R-6-F01, isolated from deep coal-bearing sediments 2306 m beneath the seafloor. This strain possesses exceptional characteristics, including the ability to thrive in extreme conditions such as high temperature (45 °C), high pressure (35 Mpa), and anaerobic environments, and exhibits broad-spectrum antimicrobial activity, producing the antibiotic penicillin at a concentration of 358 μg/mL. Genome sequencing and assembly revealed a genome size of 33.19 Mb with a GC content of 48.84%, containing 6959 coding genes. Comparative analysis with eight terrestrial strains identified 88 unique genes primarily associated with penicillin and aflatoxins biosynthesis, carbohydrate degradation, viral resistance, and three secondary metabolism gene clusters. Furthermore, significant expansions in gene families related to DNA repair were observed, likely linked to the strain's adaptation to its environmental niche. CONCLUSIONS Our findings provide insights into the genomic and biological characteristics of P. chrysogenum adaptation to extreme anaerobic subseafloor sedimentary environments, such as high temperature and pressure.
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Affiliation(s)
- Xuan Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China
| | - Xinran Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China
| | - Fan Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China
| | - Yarong Xue
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China
| | - Changhong Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, China.
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Parodi L, Comeau ME, Georgakis MK, Mayerhofer E, Chung J, Falcone GJ, Malik R, Demel SL, Worrall BB, Koch S, Testai FD, Kittner SJ, McCauley JL, Hall CE, Mayson DJ, Elkind MS, James ML, Woo D, Rosand J, Langefeld CD, Anderson CD. Deep resequencing of the 1q22 locus in non-lobar intracerebral hemorrhage. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.18.23288754. [PMID: 37162822 PMCID: PMC10168419 DOI: 10.1101/2023.04.18.23288754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Objective Genome-wide association studies have identified 1q22 as a susceptibility locus for cerebral small vessel diseases (CSVDs), including non-lobar intracerebral hemorrhage (ICH) and lacunar stroke. In the present study we performed targeted high-depth sequencing of 1q22 in ICH cases and controls to further characterize this locus and prioritize potential causal mechanisms, which remain unknown. Methods 95,000 base pairs spanning 1q22 , including SEMA4A, SLC25A44 and PMF1 / PMF1-BGLAP were sequenced in 1,055 spontaneous ICH cases (534 lobar and 521 non-lobar) and 1,078 controls. Firth regression and RIFT analysis were used to analyze common and rare variants, respectively. Chromatin interaction analyses were performed using Hi-C, ChIP-Seq and ChIA-PET databases. Multivariable Mendelian randomization (MVMR) assessed whether alterations in gene-specific expression relative to regionally co-expressed genes at 1q22 could be causally related to ICH risk. Results Common and rare variant analyses prioritized variants in SEMA4A 5'-UTR and PMF1 intronic regions, overlapping with active promoter and enhancer regions based on ENCODE annotation. Hi-C data analysis determined that 1q22 is spatially organized in a single chromatin loop and that the genes therein belong to the same Topologically Associating Domain. ChIP-Seq and ChIA-PET data analysis highlighted the presence of long-range interactions between the SEMA4A -promoter and PMF1 -enhancer regions prioritized by association testing. MVMR analyses demonstrated that PMF1 overexpression could be causally related to non-lobar ICH risk. Interpretation Altered promoter-enhancer interactions leading to PMF1 overexpression, potentially dysregulating polyamine catabolism, could explain demonstrated associations with non-lobar ICH risk at 1q22 , offering a potential new target for prevention of ICH and CSVD.
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Requena E, Alonso-Guirado L, Veloso J, Villarino M, Melgarejo P, Espeso EA, Larena I. Comparative analysis of Penicillium genomes reveals the absence of a specific genetic basis for biocontrol in Penicillium rubens strain 212. Front Microbiol 2023; 13:1075327. [PMID: 36713150 PMCID: PMC9880469 DOI: 10.3389/fmicb.2022.1075327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/06/2022] [Indexed: 01/15/2023] Open
Abstract
Penicillium rubens strain 212 (PO212) is a filamentous fungus belonging to the division Ascomycete. PO212 acts as an effective biocontrol agent against several pathogens in a variety of horticultural crops including Fusarium oxysporum f.sp. lycopersici, causing vascular wilt disease in tomato plants. We assembled draft genomes of two P. rubens strains, the biocontrol agent PO212 and the soil isolate S27, which lacks biocontrol activity. We also performed comparative analyses of the genomic sequence of PO212 with that of the other P. rubens and P. chrysogenum strains. This is the first Penicillium strain with biocontrol activity whose genome has been sequenced and compared. PO212 genome size is 2,982 Mb, which is currently organized into 65 scaffolds and a total of 10,164 predicted Open Reading Frames (ORFs). Sequencing confirmed that PO212 belongs to P. rubens clade. The comparative analysis of the PO212 genome with the genomes of other P. rubens and Penicillium chrysogenum strains available in databases showed strong conservation among genomes, but a correlation was not found between these genomic data and the biocontrol phenotype displayed by PO212. Finally, the comparative analysis between PO212 and S27 genomes showed high sequence conservation and a low number of variations mainly located in ORF regions. These differences found in coding regions between PO212 and S27 genomes can explain neither the biocontrol activity of PO212 nor the absence of such activity in S27, opening a possible avenue toward transcriptomic and epigenetic studies that may shed light on this mechanism for fighting plant diseases caused by fungal pathogens. The genome sequences described in this study provide a useful novel resource for future research into the biology, ecology, and evolution of biological control agents.
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Affiliation(s)
- Elena Requena
- Grupo Hongos Fitopatógenos, Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas (INIA-CSIC), Madrid, Spain
| | - Lola Alonso-Guirado
- Grupo de Epidemiología Genética y Molecular, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Javier Veloso
- Departamento de Biología Funcional, Escuela Politécnica Superior de Ingeniería, Universidad de Santiago de Compostela, Lugo, Spain
| | - María Villarino
- Grupo Hongos Fitopatógenos, Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas (INIA-CSIC), Madrid, Spain
| | - Paloma Melgarejo
- Grupo Hongos Fitopatógenos, Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas (INIA-CSIC), Madrid, Spain
| | - Eduardo Antonio Espeso
- Laboratorio de Biología Celular de Aspergillus, Departamento de Biología Celular y Molecular, Centro de Investigaciones Biológicas Margarita Salas, CSIC (CIB-CSIC), Madrid, Spain
| | - Inmaculada Larena
- Grupo Hongos Fitopatógenos, Departamento de Protección Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Consejo Superior de Investigaciones Científicas (INIA-CSIC), Madrid, Spain,*Correspondence: Inmaculada Larena, ✉
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Fierro F, Vaca I, Castillo NI, García-Rico RO, Chávez R. Penicillium chrysogenum, a Vintage Model with a Cutting-Edge Profile in Biotechnology. Microorganisms 2022; 10:microorganisms10030573. [PMID: 35336148 PMCID: PMC8954384 DOI: 10.3390/microorganisms10030573] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 12/20/2022] Open
Abstract
The discovery of penicillin entailed a decisive breakthrough in medicine. No other medical advance has ever had the same impact in the clinical practise. The fungus Penicillium chrysogenum (reclassified as P. rubens) has been used for industrial production of penicillin ever since the forties of the past century; industrial biotechnology developed hand in hand with it, and currently P. chrysogenum is a thoroughly studied model for secondary metabolite production and regulation. In addition to its role as penicillin producer, recent synthetic biology advances have put P. chrysogenum on the path to become a cell factory for the production of metabolites with biotechnological interest. In this review, we tell the history of P. chrysogenum, from the discovery of penicillin and the first isolation of strains with high production capacity to the most recent research advances with the fungus. We will describe how classical strain improvement programs achieved the goal of increasing production and how the development of different molecular tools allowed further improvements. The discovery of the penicillin gene cluster, the origin of the penicillin genes, the regulation of penicillin production, and a compilation of other P. chrysogenum secondary metabolites will also be covered and updated in this work.
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Affiliation(s)
- Francisco Fierro
- Departamento de Biotecnología, Universidad Autónoma Metropolitana-Unidad Iztapalapa, Ciudad de México 09340, Mexico
- Correspondence:
| | - Inmaculada Vaca
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile;
| | - Nancy I. Castillo
- Grupo de Investigación en Ciencias Biológicas y Químicas, Facultad de Ciencias, Universidad Antonio Nariño, Bogotá 110231, Colombia;
| | - Ramón Ovidio García-Rico
- Grupo de Investigación GIMBIO, Departamento De Microbiología, Facultad de Ciencias Básicas, Universidad de Pamplona, Pamplona 543050, Colombia;
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9170020, Chile;
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García-Estrada C, Martín JF, Cueto L, Barreiro C. Omics Approaches Applied to Penicillium chrysogenum and Penicillin Production: Revealing the Secrets of Improved Productivity. Genes (Basel) 2020; 11:genes11060712. [PMID: 32604893 PMCID: PMC7348727 DOI: 10.3390/genes11060712] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/07/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022] Open
Abstract
Penicillin biosynthesis by Penicillium chrysogenum is one of the best-characterized biological processes from the genetic, molecular, biochemical, and subcellular points of view. Several omics studies have been carried out in this filamentous fungus during the last decade, which have contributed to gathering a deep knowledge about the molecular mechanisms underlying improved productivity in industrial strains. The information provided by these studies is extremely useful for enhancing the production of penicillin or other bioactive secondary metabolites by means of Biotechnology or Synthetic Biology.
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Affiliation(s)
- Carlos García-Estrada
- INBIOTEC (Instituto de Biotecnología de León). Avda. Real 1—Parque Científico de León, 24006 León, Spain; (L.C.); (C.B.)
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
- Correspondence: or ; Tel.: +34-987210308
| | - Juan F. Martín
- Área de Microbiología, Departamento de Biología Molecular, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain;
| | - Laura Cueto
- INBIOTEC (Instituto de Biotecnología de León). Avda. Real 1—Parque Científico de León, 24006 León, Spain; (L.C.); (C.B.)
| | - Carlos Barreiro
- INBIOTEC (Instituto de Biotecnología de León). Avda. Real 1—Parque Científico de León, 24006 León, Spain; (L.C.); (C.B.)
- Departamento de Biología Molecular, Universidad de León, Campus de Ponferrada, Avda. Astorga s/n, 24401 Ponferrada, Spain
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Martín JF. Insight into the Genome of Diverse Penicillium chrysogenum Strains: Specific Genes, Cluster Duplications and DNA Fragment Translocations. Int J Mol Sci 2020; 21:ijms21113936. [PMID: 32486280 PMCID: PMC7312703 DOI: 10.3390/ijms21113936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/19/2020] [Accepted: 05/29/2020] [Indexed: 11/24/2022] Open
Abstract
Background: There are eighteen species within the Penicillium genus section chrysogena, including the original penicillin producers Penicillium notatum (Fleming strain) and Penicillium chrysogenum NRRL 1951. Other wild type isolates of the Penicillium genus are relevant for the production of useful proteins and primary or secondary metabolites. The aim of this article is to characterize strain specific genes and those genes which are involved in secondary metabolite biosynthesis, particularly the mutations that have been introduced during the β-lactams strain improvement programs. Results: The available genomes of several classical and novel P. chrysogenum strains have been compared. The first genome sequenced was that of the reference strain P. chrysogenum Wis54-1255, which derives from the wild type P. chrysogenum NRRL 1951; its genome size is 32.19 Mb and it encodes 12,943 proteins. Four chromosomes were resolved in P. chrysogenum and P. notatum by pulse field gel electrophoresis. The genomes of three industrial strains have a similar size but contain gene duplications and truncations; the penicillin gene cluster copy number ranges from one in the wild type to twelve in the P. chrysogenum ASP-E1 industrial strain and is organized in head to tail tandem repeats. The genomes of two new strains, P. chrysogenum KF-25, a producer of antifungal proteins isolated from a soil sample, and P. chrysogenum HKF2, a strain with carbohydrate-converting activities isolated from a sludge treatment plant, showed strain specific genes. Conclusions: The overall comparison of all available P. chrysogenum genomes indicates that there are a significant number of strain-specific genes, mutations of structural and regulatory genes, gene cluster duplications and DNA fragment translocations. This information provides important leads to improve the biosynthesis of enzymes, antifungal agents, prebiotics or different types of secondary metabolites.
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Affiliation(s)
- Juan F Martín
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, 24071 León, Spain
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Jurick WM, Peng H, Beard HS, Garrett WM, Lichtner FJ, Luciano-Rosario D, Macarisin O, Liu Y, Peter KA, Gaskins VL, Yang T, Mowery J, Bauchan G, Keller NP, Cooper B. Blistering1 Modulates Penicillium expansum Virulence Via Vesicle-mediated Protein Secretion. Mol Cell Proteomics 2020; 19:344-361. [PMID: 31871254 PMCID: PMC7000123 DOI: 10.1074/mcp.ra119.001831] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/15/2019] [Indexed: 11/06/2022] Open
Abstract
The blue mold fungus, Penicillium expansum, is a postharvest apple pathogen that contributes to food waste by rotting fruit and by producing harmful mycotoxins (e.g. patulin). To identify genes controlling pathogen virulence, a random T-DNA insertional library was created from wild-type P. expansum strain R19. One transformant, T625, had reduced virulence in apples, blistered mycelial hyphae, and a T-DNA insertion that abolished transcription of the single copy locus in which it was inserted. The gene, Blistering1, encodes a protein with a DnaJ domain, but otherwise has little homology outside the Aspergillaceae, a family of fungi known for producing antibiotics, mycotoxins, and cheese. Because protein secretion is critical for these processes and for host infection, mass spectrometry was used to monitor proteins secreted into liquid media during fungal growth. T625 failed to secrete a set of enzymes that degrade plant cell walls, along with ones that synthesize the three final biosynthetic steps of patulin. Consequently, the culture broth of T625 had significantly reduced capacity to degrade apple tissue and contained 30 times less patulin. Quantitative mass spectrometry of 3,282 mycelial proteins revealed that T625 had altered cellular networks controlling protein processing in the endoplasmic reticulum, protein export, vesicle-mediated transport, and endocytosis. T625 also had reduced proteins controlling mRNA surveillance and RNA processing. Transmission electron microscopy of hyphal cross sections confirmed that T625 formed abnormally enlarged endosomes or vacuoles. These data reveal that Blistering1 affects internal and external protein processing involving vesicle-mediated transport in a family of fungi with medical, commercial, and agricultural importance.
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Affiliation(s)
- Wayne M Jurick
- USDA-ARS, Food Quality Laboratory, Beltsville Agricultural Research Center, Beltsville, Maryland.
| | - Hui Peng
- USDA-ARS, Food Quality Laboratory, Beltsville Agricultural Research Center, Beltsville, Maryland
| | - Hunter S Beard
- USDA-ARS, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Beltsville, Maryland
| | - Wesley M Garrett
- USDA-ARS, Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, Beltsville, Maryland
| | - Franz J Lichtner
- USDA-ARS, Food Quality Laboratory, Beltsville Agricultural Research Center, Beltsville, Maryland; Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee 37830
| | - Dianiris Luciano-Rosario
- University of Wisconsin, Department of Medical Microbiology and Immunology and Bacteriology, Madison, Wisconsin
| | - Otilia Macarisin
- USDA-ARS, Food Quality Laboratory, Beltsville Agricultural Research Center, Beltsville, Maryland
| | - Yingjian Liu
- USDA-ARS, Food Quality Laboratory, Beltsville Agricultural Research Center, Beltsville, Maryland
| | - Kari A Peter
- Penn State University, Department of Plant Pathology and Environmental Microbiology, Fruit Research and Extension Center, Biglerville, Pennsylvania
| | - Verneta L Gaskins
- USDA-ARS, Food Quality Laboratory, Beltsville Agricultural Research Center, Beltsville, Maryland
| | - Tianbao Yang
- USDA-ARS, Food Quality Laboratory, Beltsville Agricultural Research Center, Beltsville, Maryland
| | - Joseph Mowery
- USDA-ARS, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Beltsville, Maryland
| | - Gary Bauchan
- USDA-ARS, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Beltsville, Maryland
| | - Nancy P Keller
- University of Wisconsin, Department of Medical Microbiology and Immunology and Bacteriology, Madison, Wisconsin
| | - Bret Cooper
- USDA-ARS, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Beltsville, Maryland
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11
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Barreiro C, García-Estrada C. Proteomics and Penicillium chrysogenum: Unveiling the secrets behind penicillin production. J Proteomics 2018; 198:119-131. [PMID: 30414515 DOI: 10.1016/j.jprot.2018.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/27/2018] [Accepted: 11/05/2018] [Indexed: 01/29/2023]
Abstract
Discovery, industrial production and clinical applications of penicillin, together with scientific findings on penicillin biosynthesis and its complex regulation, are model milestones of the historical evolution of the most recognized 'magic bullet' against microbial infections available in the worldwide market. Thousands of tons of penicillin produced nowadays are the result of a huge number of technical, industrial and scientific tackled and solved challenges. This combination of, sometimes unsuspected, findings has given Proteomics the chance to support the understanding of the physiology of the high-producing fungal strains and the development of enhanced mutants by means of inverse engineering. Thus, this review, which is part of the special issue entitled "A Tribute to J. Proteomics on its 10th Anniversary", describes how Proteomics has contributed to characterize different aspects related to penicillin production in Penicillium chrosogenum. It covers from global proteome characterizations (intracellular, extracellular and microbodies) to proteome-wide comparative analyses between different penicillin-producing mutant strains and conditions, paying special attention to the methodologies used, as well as to the most important outcomes. As a result, a guide of Proteomics approaches applied to the characterization of penicillin production by P. chrysogenum is detailed in the birthday of the Fleming's most relevant finding. SIGNIFICANCE: Although the discovery of penicillin is celebrating the 90th birthday and its clinical application is worldwide recognized, in fact, semisynthetic penicillins are still one of the most prescribed antibiotics, only the arrival of the post-genomic era during the first decade of the 21st century, and more precisely the Proteomics approaches, have contributed to unveil the industrial secrets behind penicillin production. This review provides relevant information, based on proteomics studies, about the molecular mechanisms responsible for increased penicillin titres, and therefore, may represent a clear model of inverse engineering in microorganisms.
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Affiliation(s)
- Carlos Barreiro
- INBIOTEC (Instituto de Biotecnología de León), Avda. Real 1 - Parque Científico de León, 24006 León, Spain; Departamento de Biología Molecular, Universidad de León, Campus de Ponferrada, Avda. Astorga s/n, 24401 Ponferrada, Spain.
| | - Carlos García-Estrada
- INBIOTEC (Instituto de Biotecnología de León), Avda. Real 1 - Parque Científico de León, 24006 León, Spain; Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
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Integrated whole-genome and transcriptome sequence analysis reveals the genetic characteristics of a riboflavin-overproducing Bacillus subtilis. Metab Eng 2018; 48:138-149. [DOI: 10.1016/j.ymben.2018.05.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 05/17/2018] [Accepted: 05/31/2018] [Indexed: 11/23/2022]
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Li J, Gu F, Wu R, Yang J, Zhang KQ. Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi. Sci Rep 2017; 7:45456. [PMID: 28358043 PMCID: PMC5371821 DOI: 10.1038/srep45456] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/28/2017] [Indexed: 01/10/2023] Open
Abstract
Subtilases belong to a superfamily of serine proteases which are ubiquitous in fungi and are suspected to have developed distinct functional properties to help fungi adapt to different ecological niches. In this study, we conducted a large-scale phylogenomic survey of subtilase protease genes in 83 whole genome sequenced fungal species in order to identify the evolutionary patterns and subsequent functional divergences of different subtilase families among the main lineages of the fungal kingdom. Our comparative genomic analyses of the subtilase superfamily indicated that extensive gene duplications, losses and functional diversifications have occurred in fungi, and that the four families of subtilase enzymes in fungi, including proteinase K-like, Pyrolisin, kexin and S53, have distinct evolutionary histories which may have facilitated the adaptation of fungi to a broad array of life strategies. Our study provides new insights into the evolution of the subtilase superfamily in fungi and expands our understanding of the evolution of fungi with different lifestyles.
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Affiliation(s)
- Juan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
| | - Fei Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
| | - Runian Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
| | - JinKui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, P.R. China
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Identification of Mycobacterial RplJ/L10 and RpsA/S1 Proteins as Novel Targets for CD4 + T Cells. Infect Immun 2017; 85:IAI.01023-16. [PMID: 28115505 PMCID: PMC5364311 DOI: 10.1128/iai.01023-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/13/2017] [Indexed: 12/20/2022] Open
Abstract
Tuberculosis (TB) due to Mycobacterium tuberculosis remains a major global infectious disease problem, and a more efficacious vaccine is urgently needed for the control and prevention of disease caused by this organism. We previously reported that a genetically modified strain of Mycobacterium smegmatis called IKEPLUS is a promising TB vaccine candidate. Since protective immunity induced by IKEPLUS is dependent on antigen-specific CD4+ T cell memory, we hypothesized that the specificity of the CD4+ T cell response was a critical feature of this protection. Using in vitro assays of interferon gamma production (enzyme-linked immunosorbent spot [ELISPOT] assays) by splenocytes from IKEPLUS-immunized C57BL/6J mice, we identified an immunogenic peptide within the mycobacterial ribosomal large subunit protein RplJ, encoded by the Rv0651 gene. In a complementary approach, we generated major histocompatibility complex (MHC) class II-restricted T cell hybridomas from IKEPLUS-immunized mice. Screening of these T cell hybridomas against IKEPLUS and ribosomes enriched from IKEPLUS suggested that the CD4+ T cell response in IKEPLUS-immunized mice was dominated by the recognition of multiple components of the mycobacterial ribosome. Importantly, CD4+ T cells specific for mycobacterial ribosomes accumulate to significant levels in the lungs of IKEPLUS-immunized mice following aerosol challenge with virulent M. tuberculosis, consistent with a role for these T cells in protective host immunity in TB. The identification of CD4+ T cell responses to defined ribosomal protein epitopes expands the range of antigenic targets for adaptive immune responses to M. tuberculosis and may help to inform the design of more effective vaccines against tuberculosis.
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Ziemons S, Koutsantas K, Becker K, Dahlmann T, Kück U. Penicillin production in industrial strain Penicillium chrysogenum P2niaD18 is not dependent on the copy number of biosynthesis genes. BMC Biotechnol 2017; 17:16. [PMID: 28209150 PMCID: PMC5314624 DOI: 10.1186/s12896-017-0335-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/09/2017] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Multi-copy gene integration into microbial genomes is a conventional tool for obtaining improved gene expression. For Penicillium chrysogenum, the fungal producer of the beta-lactam antibiotic penicillin, many production strains carry multiple copies of the penicillin biosynthesis gene cluster. This discovery led to the generally accepted view that high penicillin titers are the result of multiple copies of penicillin genes. Here we investigated strain P2niaD18, a production line that carries only two copies of the penicillin gene cluster. RESULTS We performed pulsed-field gel electrophoresis (PFGE), quantitative qRT-PCR, and penicillin bioassays to investigate production, deletion and overexpression strains generated in the P. chrysogenum P2niaD18 background, in order to determine the copy number of the penicillin biosynthesis gene cluster, and study the expression of one penicillin biosynthesis gene, and the penicillin titer. Analysis of production and recombinant strain showed that the enhanced penicillin titer did not depend on the copy number of the penicillin gene cluster. Our assumption was strengthened by results with a penicillin null strain lacking pcbC encoding isopenicillin N synthase. Reintroduction of one or two copies of the cluster into the pcbC deletion strain restored transcriptional high expression of the pcbC gene, but recombinant strains showed no significantly different penicillin titer compared to parental strains. CONCLUSIONS Here we present a molecular genetic analysis of production and recombinant strains in the P2niaD18 background carrying different copy numbers of the penicillin biosynthesis gene cluster. Our analysis shows that the enhanced penicillin titer does not strictly depend on the copy number of the cluster. Based on these overall findings, we hypothesize that instead, complex regulatory mechanisms are prominently implicated in increased penicillin biosynthesis in production strains.
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Affiliation(s)
- Sandra Ziemons
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, ND7/131, Universitätsstraße 150, 44780, Bochum, Germany
| | - Katerina Koutsantas
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, ND7/131, Universitätsstraße 150, 44780, Bochum, Germany
| | - Kordula Becker
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, ND7/131, Universitätsstraße 150, 44780, Bochum, Germany
| | - Tim Dahlmann
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, ND7/131, Universitätsstraße 150, 44780, Bochum, Germany
| | - Ulrich Kück
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, ND7/131, Universitätsstraße 150, 44780, Bochum, Germany.
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Julca I, Droby S, Sela N, Marcet-Houben M, Gabaldón T. Contrasting Genomic Diversity in Two Closely Related Postharvest Pathogens: Penicillium digitatum and Penicillium expansum. Genome Biol Evol 2015; 8:218-27. [PMID: 26672008 PMCID: PMC4758248 DOI: 10.1093/gbe/evv252] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Penicillium digitatum and Penicillium expansum are two closely related fungal plant pathogens causing green and blue mold in harvested fruit, respectively. The two species differ in their host specificity, being P. digitatum restricted to citrus fruits and P. expansum able to infect a wide range of fruits after harvest. Although host-specific Penicillium species have been found to have a smaller gene content, it is so far unclear whether these different host specificities impact genome variation at the intraspecific level. Here we assessed genome variation across four P. digitatum and seven P. expansum isolates from geographically distant regions. Our results show very high similarity (average 0.06 SNPs [single nucleotide polymorphism] per kb) between globally distributed isolates of P. digitatum pointing to a recent expansion of a single lineage. This low level of genetic variation found in our samples contrasts with the higher genetic variability observed in the similarly distributed P. expansum isolates (2.44 SNPs per kb). Patterns of polymorphism in P. expansum indicate that recombination exists between genetically diverged strains. Consistent with the existence of sexual recombination and heterothallism, which was unknown for this species, we identified the two alternative mating types in different P. expansum isolates. Patterns of polymorphism in P. digitatum indicate a recent clonal population expansion of a single lineage that has reached worldwide distribution. We suggest that the contrasting patterns of genomic variation between the two species reflect underlying differences in population dynamics related with host specificities and related agricultural practices. It should be noted, however, that this results should be confirmed with a larger sampling of strains, as new strains may broaden the diversity so far found in P. digitatum.
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Affiliation(s)
- Irene Julca
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Universitat Autònoma De Barcelona, Spain
| | - Samir Droby
- Department of Postharvest Science, ARO, the Volcani Center, Bet Dagan, Israel
| | - Noa Sela
- Department of Plant Pathology and Weed Research, The Volcani Center, Bet Dagan, Israel
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana De Recerca I Estudis Avançats (ICREA), Barcelona, Spain
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Exploiting the genome sequence of Streptomyces nodosus for enhanced antibiotic production. Appl Microbiol Biotechnol 2015; 100:1285-1295. [PMID: 26497174 DOI: 10.1007/s00253-015-7060-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 09/24/2015] [Accepted: 10/02/2015] [Indexed: 10/22/2022]
Abstract
The genome of the amphotericin producer Streptomyces nodosus was sequenced. A single scaffold of 7,714,110 bp was obtained. Biosynthetic genes were identified for several natural products including polyketides, peptides, siderophores and terpenes. The majority of these clusters specified known compounds. Most were silent or expressed at low levels and unlikely to compete with amphotericin production. Biosynthesis of a skyllamycin analogue was activated by introducing expression plasmids containing either a gene for a LuxR transcriptional regulator or genes for synthesis of the acyl moiety of the lipopeptide. In an attempt to boost amphotericin production, genes for acyl CoA carboxylases, a phosphopantetheinyl transferase and the AmphRIV transcriptional activator were overexpressed, and the effects on yields were investigated. This study provides the groundwork for metabolic engineering of S. nodosus strains to produce high yields of amphotericin analogues.
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Prauße MTE, Schäuble S, Guthke R, Schuster S. Computing the various pathways of penicillin synthesis and their molar yields. Biotechnol Bioeng 2015; 113:173-81. [PMID: 26134880 DOI: 10.1002/bit.25694] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 06/05/2015] [Accepted: 06/22/2015] [Indexed: 11/09/2022]
Abstract
More than 80 years after its discovery, penicillin is still a widely used and commercially highly important antibiotic. Here, we analyse the metabolic network of penicillin synthesis in Penicillium chrysogenum based on the concept of elementary flux modes. In particular, we consider the synthesis of the invariant molecular core of the various subtypes of penicillin and the two major ways of incorporating sulfur: transsulfuration and direct sulfhydrylation. 66 elementary modes producing this invariant core are obtained. These show four different yields with respect to glucose, notably ½, 2/5, 1/3, and 2/7, with the highest yield of ½ occurring only when direct sulfhydrylation is used and α-aminoadipate is completely recycled. In the case of no recycling of this intermediate, we find the maximum yield to be 2/7. We compare these values with earlier literature values. Our analysis provides a systematic overview of the redundancy in penicillin synthesis and a detailed insight into the corresponding routes. Moreover, we derive suggestions for potential knockouts that could increase the average yield.
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Affiliation(s)
- Maria T E Prauße
- Department of Bioinformatics, University of Jena, Ernst-Abbe-Pl. 2, 07743 Jena, Germany.,Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
| | - Sascha Schäuble
- Jena University Language & Information Engineering Lab, Jena, Germany
| | - Reinhard Guthke
- Leibniz-Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
| | - Stefan Schuster
- Department of Bioinformatics, University of Jena, Ernst-Abbe-Pl. 2, 07743 Jena, Germany.
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Affiliation(s)
- Krishna Kant Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
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Improvement of Aspergillus nidulans penicillin production by targeting AcvA to peroxisomes. Metab Eng 2014; 25:131-9. [DOI: 10.1016/j.ymben.2014.07.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/03/2014] [Accepted: 07/09/2014] [Indexed: 11/21/2022]
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