title: Comparative genomics revealed key molecular targets to rapidly convert a reference rifamycin-producing bacterial strain into an overproducer by genetic engineering.
abstract: Rifamycins are mainstay agents in treatment of many widespread diseases, but how an improved rifamycin producer can be created is still incompletely understood. Here, we describe a comparative genomic approach to investigate the mutational patterns introduced by the classical mutate-and-screen method in the genome of an improved rifamycin producer. Comparing the genome of the rifamycin B overproducer Amycolatopsis mediterranei HP-130 with those of the reference strains A. mediterranei S699 and U32, we identified 250 variations, affecting 227 coding sequences (CDS), 109 of which were HP-130-specific since they were absent in both S699 and U32. Mutational and transcriptional patterns indicated a series of genomic manipulations that not only proved the causative effect of mutB2 (coding for methylmalonyl-CoA mutase large subunit) and argS2 (coding for arginyl tRNA synthetase) mutations on the overproduction of rifamycin, but also constituted a rational strategy to genetically engineer a reference strain into an overproducer.
authors.affiliation: Institute of Biomedical Technologies, National Research Council, Segrate, Milan 20090, Italy.
authors.forename: Clelia
authors.initials: C
authors.lastname: Peano
authors.affiliation: Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce 73100, Italy.
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Damiano
authors.affiliation: Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena 40125, Italy.
authors.forename: Mattia
authors.initials: M
authors.lastname: Forcato
authors.affiliation: Institute of Biomedical Technologies, National Research Council, Segrate, Milan 20090, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Pietrelli
authors.affiliation: Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce 73100, Italy.
authors.forename: Carla
authors.initials: C
authors.lastname: Palumbo
authors.affiliation: Institute of Biomedical Technologies, National Research Council, Segrate, Milan 20090, Italy.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Corti
authors.affiliation: Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce 73100, Italy.
authors.forename: Luisa
authors.initials: L
authors.lastname: Siculella
authors.affiliation: Institute of Biomedical Technologies, National Research Council, Segrate, Milan 20090, Italy.
authors.forename: Fabio
authors.initials: F
authors.lastname: Fuligni
authors.affiliation: Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena 40125, Italy.
authors.forename: Guidantonio Malagoli
authors.initials: GM
authors.lastname: Tagliazucchi
authors.affiliation: Laboratory of Analytical and Isotopic Mass Spectrometry, Department of Cultural Heritage, University of Salento, Lecce 73100, Italy.
authors.forename: Giuseppe Egidio
authors.initials: GE
authors.lastname: De Benedetto
authors.affiliation: Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena 40125, Italy.
authors.forename: Silvio
authors.initials: S
authors.lastname: Bicciato
authors.affiliation: Institute of Biomedical Technologies, National Research Council, Segrate, Milan 20090, Italy.
authors.forename: Gianluca
authors.initials: G
authors.lastname: De Bellis
authors.affiliation: Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce 73100, Italy. Electronic address: pietro.alifano@unisalento.it.
authors.forename: Pietro
authors.initials: P
authors.lastname: Alifano
mesh_terms: D039903:Actinobacteria / Q000145:classification / Q000235:genetics*; D001126:Arginine-tRNA Ligase / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods; D055028:Comparative Genomic Hybridization / Q000379:methods; D018390:Gene Targeting / Q000379:methods; D024861:Genetic Enhancement / Q000379:methods; D016680:Genome, Bacterial / Q000235:genetics*; D060847:Metabolic Engineering / Q000379:methods*; D008765:Methylmalonyl-CoA Mutase / Q000235:genetics*; D012294:Rifamycins / Q000378:metabolism*; D013045:Species Specificity; D015854:Up-Regulation / Q000235:genetics
chemical_list: D012294:Rifamycins; C033974:rifamycin B; D008765:Methylmalonyl-CoA Mutase; D001126:Arginine-tRNA Ligase
keywords: Amycolatopsis mediterranei; Arginyl tRNA synthetase; Methylmalonyl-CoA mutase; Rifamycin; Strain improvement