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Kunakom S, Otani H, Udwary DW, Doering DT, Mouncey NJ. Cytochromes P450 involved in Bacterial RiPP Biosyntheses. J Ind Microbiol Biotechnol 2023; 50:7080148. [PMID: 36931895 PMCID: PMC10124130 DOI: 10.1093/jimb/kuad005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/14/2023] [Indexed: 03/19/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a large class of secondary metabolites that have garnered scientific attention due to their complex scaffolds with potential roles in medicine, agriculture, and chemical ecology. RiPPs derive from the cleavage of ribosomally-synthesized proteins and the additional modifications, catalyzed by various enzymes to alter the peptide backbone or side chains. Of these enzymes, cytochromes P450 are a superfamily of heme-thiolate proteins involved in many metabolic pathways, including RiPP biosyntheses. In this review, we focus our discussion on cytochromes P450 involved in RiPP pathways and the unique chemical transformations they mediate. Previous studies have revealed a wealth of cytochromes P450 distributed across all domains of life. While the number of characterized cytochromes P450 involved in RiPP biosyntheses is relatively small, they catalyze various enzymatic reactions such as C-C or C-N bond formation. Formation of some RiPPs is catalyzed by more than one cytochrome P450, enabling structural diversity. With the continuous improvement of the bioinformatic tools for RiPP prediction and advancement in synthetic biology techniques, it is expected that further cytochrome P450-mediated RiPP biosynthetic pathways will be discovered.
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Affiliation(s)
| | - Hiroshi Otani
- US Department of Energy Joint Genome Institute.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Daniel W Udwary
- US Department of Energy Joint Genome Institute.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Nigel J Mouncey
- US Department of Energy Joint Genome Institute.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Kominek J, Doering DT, Opulente DA, Shen XX, Zhou X, DeVirgilio J, Hulfachor AB, Groenewald M, Mcgee MA, Karlen SD, Kurtzman CP, Rokas A, Hittinger CT. Eukaryotic Acquisition of a Bacterial Operon. Cell 2019; 176:1356-1366.e10. [PMID: 30799038 DOI: 10.1016/j.cell.2019.01.034] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/20/2018] [Accepted: 01/23/2019] [Indexed: 01/01/2023]
Abstract
Operons are a hallmark of bacterial genomes, where they allow concerted expression of functionally related genes as single polycistronic transcripts. They are rare in eukaryotes, where each gene usually drives expression of its own independent messenger RNAs. Here, we report the horizontal operon transfer of a siderophore biosynthesis pathway from relatives of Escherichia coli into a group of budding yeast taxa. We further show that the co-linearly arranged secondary metabolism genes are expressed, exhibit eukaryotic transcriptional features, and enable the sequestration and uptake of iron. After transfer, several genetic changes occurred during subsequent evolution, including the gain of new transcription start sites that were sometimes within protein-coding sequences, acquisition of polyadenylation sites, structural rearrangements, and integration of eukaryotic genes into the cluster. We conclude that the genes were likely acquired as a unit, modified for eukaryotic gene expression, and maintained by selection to adapt to the highly competitive, iron-limited environment.
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Affiliation(s)
- Jacek Kominek
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Drew T Doering
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA; Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Dana A Opulente
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, 510642 Guangzhou, China
| | - Jeremy DeVirgilio
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604, USA
| | - Amanda B Hulfachor
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Mcsean A Mcgee
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Steven D Karlen
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Cletus P Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA; Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Shen XX, Opulente DA, Kominek J, Zhou X, Steenwyk JL, Buh KV, Haase MAB, Wisecaver JH, Wang M, Doering DT, Boudouris JT, Schneider RM, Langdon QK, Ohkuma M, Endoh R, Takashima M, Manabe RI, Čadež N, Libkind D, Rosa CA, DeVirgilio J, Hulfachor AB, Groenewald M, Kurtzman CP, Hittinger CT, Rokas A. Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum. Cell 2018; 175:1533-1545.e20. [PMID: 30415838 DOI: 10.1016/j.cell.2018.10.023] [Citation(s) in RCA: 302] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/12/2018] [Accepted: 10/04/2018] [Indexed: 11/17/2022]
Abstract
Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as genetically diverse as plants or animals. To understand budding yeast evolution, we analyzed the genomes of 332 yeast species, including 220 newly sequenced ones, which represent nearly one-third of all known budding yeast diversity. Here, we establish a robust genus-level phylogeny comprising 12 major clades, infer the timescale of diversification from the Devonian period to the present, quantify horizontal gene transfer (HGT), and reconstruct the evolution of 45 metabolic traits and the metabolic toolkit of the budding yeast common ancestor (BYCA). We infer that BYCA was metabolically complex and chronicle the tempo and mode of genomic and phenotypic evolution across the subphylum, which is characterized by very low HGT levels and widespread losses of traits and the genes that control them. More generally, our results argue that reductive evolution is a major mode of evolutionary diversification.
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Affiliation(s)
- Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Dana A Opulente
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jacek Kominek
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, 510642 Guangzhou, China
| | - Jacob L Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Kelly V Buh
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Max A B Haase
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA; Sackler Institute of Graduate Biomedical Sciences, NYU School of Medicine, New York, NY 10016, USA
| | - Jennifer H Wisecaver
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Department of Biochemistry, Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Mingshuang Wang
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Drew T Doering
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - James T Boudouris
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Rachel M Schneider
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Quinn K Langdon
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Rikiya Endoh
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Masako Takashima
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan
| | - Ri-Ichiroh Manabe
- Division of Genomic Technologies, RIKEN Center For Life Science Technologies, Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Neža Čadež
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada y Biotecnología, Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, 8400 Bariloche, Argentina
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, CP 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Jeremy DeVirgilio
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Cletus P Kurtzman
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
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Book AJ, Lewin GR, McDonald BR, Takasuka TE, Wendt-Pienkowski E, Doering DT, Suh S, Raffa KF, Fox BG, Currie CR. Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression. PLoS Biol 2016; 14:e1002475. [PMID: 27276034 PMCID: PMC4898821 DOI: 10.1371/journal.pbio.1002475] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 05/05/2016] [Indexed: 11/23/2022] Open
Abstract
The evolution of cellulose degradation was a defining event in the history of life. Without efficient decomposition and recycling, dead plant biomass would quickly accumulate and become inaccessible to terrestrial food webs and the global carbon cycle. On land, the primary drivers of plant biomass deconstruction are fungi and bacteria in the soil or associated with herbivorous eukaryotes. While the ecological importance of plant-decomposing microbes is well established, little is known about the distribution or evolution of cellulolytic activity in any bacterial genus. Here we show that in Streptomyces, a genus of Actinobacteria abundant in soil and symbiotic niches, the ability to rapidly degrade cellulose is largely restricted to two clades of host-associated strains and is not a conserved characteristic of the Streptomyces genus or host-associated strains. Our comparative genomics identify that while plant biomass degrading genes (CAZy) are widespread in Streptomyces, key enzyme families are enriched in highly cellulolytic strains. Transcriptomic analyses demonstrate that cellulolytic strains express a suite of multi-domain CAZy enzymes that are coregulated by the CebR transcriptional regulator. Using targeted gene deletions, we verify the importance of a highly expressed cellulase (GH6 family cellobiohydrolase) and the CebR transcriptional repressor to the cellulolytic phenotype. Evolutionary analyses identify complex genomic modifications that drive plant biomass deconstruction in Streptomyces, including acquisition and selective retention of CAZy genes and transcriptional regulators. Our results suggest that host-associated niches have selected some symbiotic Streptomyces for increased cellulose degrading activity and that symbiotic bacteria are a rich biochemical and enzymatic resource for biotechnology. Cellulose deconstruction helps shape the global carbon cycle; this study shows that high cellulolytic ability evolved in select lineages of the bacterial genus Streptomyces through key changes in gene content and transcriptional regulation. Only specific microbes can deconstruct the vast stores of carbon within plant biomass. Studying the distribution, diversity, and evolution of these cellulolytic organisms improves our understanding of the ecological functions of microbes in the environment and their contributions to the global carbon cycle. The bacterial genus Streptomyces is abundant in soil, appears to readily form symbiotic associations with eukaryotic hosts, and has long been thought to contribute to plant biomass degradation. Here, we show that the ability to rapidly deconstruct cellulose is surprisingly rare in the genus Streptomyces but is enriched in symbiotic stains associated with diverse insect hosts that feed on plant biomass. By using a combination of genomic, transcriptomic, and genetic analyses, we identify key changes in gene content and expression that confer cellulolytic activity. Our results support the idea that a complex interplay of genomic changes, occurring over ancient time scales, shapes the evolution of the ecologically important ability to deconstruct plant biomass.
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Affiliation(s)
- Adam J. Book
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Gina R. Lewin
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Bradon R. McDonald
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Taichi E. Takasuka
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Evelyn Wendt-Pienkowski
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Drew T. Doering
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Steven Suh
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kenneth F. Raffa
- Department of Entomology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Brian G. Fox
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Cameron R. Currie
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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