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Nyerges A, Chiappino-Pepe A, Budnik B, Baas-Thomas M, Flynn R, Yan S, Ostrov N, Liu M, Wang M, Zheng Q, Hu F, Chen K, Rudolph A, Chen D, Ahn J, Spencer O, Ayalavarapu V, Tarver A, Harmon-Smith M, Hamilton M, Blaby I, Yoshikuni Y, Hajian B, Jin A, Kintses B, Szamel M, Seregi V, Shen Y, Li Z, Church GM. Synthetic genomes unveil the effects of synonymous recoding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.16.599206. [PMID: 38915524 PMCID: PMC11195188 DOI: 10.1101/2024.06.16.599206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Engineering the genetic code of an organism provides the basis for (i) making any organism safely resistant to natural viruses and (ii) preventing genetic information flow into and out of genetically modified organisms while (iii) allowing the biosynthesis of genetically encoded unnatural polymers1-4. Achieving these three goals requires the reassignment of multiple of the 64 codons nature uses to encode proteins. However, synonymous codon replacement-recoding-is frequently lethal, and how recoding impacts fitness remains poorly explored. Here, we explore these effects using whole-genome synthesis, multiplexed directed evolution, and genome-transcriptome-translatome-proteome co-profiling on multiple recoded genomes. Using this information, we assemble a synthetic Escherichia coli genome in seven sections using only 57 codons to encode proteins. By discovering the rules responsible for the lethality of synonymous recoding and developing a data-driven multi-omics-based genome construction workflow that troubleshoots synthetic genomes, we overcome the lethal effects of 62,007 synonymous codon swaps and 11,108 additional genomic edits. We show that synonymous recoding induces transcriptional noise including new antisense RNAs, leading to drastic transcriptome and proteome perturbation. As the elimination of select codons from an organism's genetic code results in the widespread appearance of cryptic promoters, we show that synonymous codon choice may naturally evolve to minimize transcriptional noise. Our work provides the first genome-scale description of how synonymous codon changes influence organismal fitness and paves the way for the construction of functional genomes that provide genetic firewalls from natural ecosystems and safely produce biopolymers, drugs, and enzymes with an expanded chemistry.
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Affiliation(s)
- Akos Nyerges
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Bogdan Budnik
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | | | - Regan Flynn
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Shirui Yan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- BGI Research, Shenzhen 518083, China
| | - Nili Ostrov
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Min Liu
- GenScript USA Inc., Piscataway, NJ 08854, USA
| | | | | | | | | | - Alexandra Rudolph
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Dawn Chen
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jenny Ahn
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Owen Spencer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Angela Tarver
- DOE Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Miranda Harmon-Smith
- DOE Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthew Hamilton
- DOE Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ian Blaby
- DOE Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yasuo Yoshikuni
- DOE Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Behnoush Hajian
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Adeline Jin
- GenScript USA Inc., Piscataway, NJ 08854, USA
| | - Balint Kintses
- Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, 6726, Hungary
| | - Monika Szamel
- Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, 6726, Hungary
| | - Viktoria Seregi
- Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, 6726, Hungary
| | - Yue Shen
- BGI Research, Shenzhen 518083, China
- BGI Research, Changzhou 213299, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen 518083, China
| | - Zilong Li
- GenScript USA Inc., Piscataway, NJ 08854, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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Ookubo M, Tashiro Y, Asano K, Kamei Y, Tanaka Y, Honda T, Yokoyama T, Honda M. "Rich arginine and strong positive charge" antimicrobial protein protamine: From its action on cell membranes to inhibition of bacterial vital functions. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184323. [PMID: 38614236 DOI: 10.1016/j.bbamem.2024.184323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/15/2024] [Accepted: 04/05/2024] [Indexed: 04/15/2024]
Abstract
Protamine, an antimicrobial protein derived from salmon sperm with a molecular weight of approximately 5 kDa, is composed of 60-70 % arginine and is a highly charged protein. Here, we investigated the mechanism of antimicrobial action of protamine against Cutibacterium acnes (C. acnes) focusing on its rich arginine content and strong positive charge. Especially, we focused on the attribution of dual mechanisms of antimicrobial protein, including membrane disruption or interaction with intracellular components. We first determined the dose-dependent antibacterial activity of protamine against C. acnes. In order to explore the interaction between bacterial membrane and protamine, we analyzed cell morphology, zeta potential, membrane permeability, and the composition of membrane fatty acid. In addition, the localization of protamine in bacteria was observed using fluorescent-labeled protamine. For investigation of the intracellular targets of protamine, bacterial translation was examined using a cell-free translation system. Based on our results, the mechanism of the antimicrobial action of protamine against C. acnes is as follows: 1) electrostatic interactions with the bacterial cell membrane; 2) self-internalization into the bacterial cell by changing the composition of the bacterial membrane; and 3) inhibition of bacterial growth by blocking translation inside the bacteria. However, owing to its strong electric charge, protamine can also interact with DNA, RNA, and other proteins inside the bacteria, and may inhibit various bacterial life processes beyond the translation process.
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Affiliation(s)
- Momoka Ookubo
- Graduate School of Science and Technology, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki 214-8571, Kanagawa, Japan
| | - Yuka Tashiro
- Graduate School of Science and Technology, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki 214-8571, Kanagawa, Japan
| | - Kosuke Asano
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai 980-8577, Japan
| | - Yoshiharu Kamei
- Graduate School of Science and Technology, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki 214-8571, Kanagawa, Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai 980-8577, Japan; The advanced center for innovations in next-generation medicine (INGEM), Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Takayuki Honda
- Graduate School of Science and Technology, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki 214-8571, Kanagawa, Japan
| | - Takeshi Yokoyama
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai 980-8577, Japan; The advanced center for innovations in next-generation medicine (INGEM), Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Michiyo Honda
- Graduate School of Science and Technology, Meiji University, 1-1-1, Higashimita, Tama-ku, Kawasaki 214-8571, Kanagawa, Japan.
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Frumkin I, Laub MT. Selection of a de novo gene that can promote survival of Escherichia coli by modulating protein homeostasis pathways. Nat Ecol Evol 2023; 7:2067-2079. [PMID: 37945946 PMCID: PMC10697842 DOI: 10.1038/s41559-023-02224-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 09/12/2023] [Indexed: 11/12/2023]
Abstract
Cellular novelty can emerge when non-functional loci become functional genes in a process termed de novo gene birth. But how proteins with random amino acid sequences beneficially integrate into existing cellular pathways remains poorly understood. We screened ~108 genes, generated from random nucleotide sequences and devoid of homology to natural genes, for their ability to rescue growth arrest of Escherichia coli cells producing the ribonuclease toxin MazF. We identified ~2,000 genes that could promote growth, probably by reducing transcription from the promoter driving toxin expression. Additionally, one random protein, named Random antitoxin of MazF (RamF), modulated protein homeostasis by interacting with chaperones, leading to MazF proteolysis and a consequent loss of its toxicity. Finally, we demonstrate that random proteins can improve during evolution by identifying beneficial mutations that turned RamF into a more efficient inhibitor. Our work provides a mechanistic basis for how de novo gene birth can produce functional proteins that effectively benefit cells evolving under stress.
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Affiliation(s)
- Idan Frumkin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
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Simoens L, Fijalkowski I, Van Damme P. Exposing the small protein load of bacterial life. FEMS Microbiol Rev 2023; 47:fuad063. [PMID: 38012116 PMCID: PMC10723866 DOI: 10.1093/femsre/fuad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/10/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023] Open
Abstract
The ever-growing repertoire of genomic techniques continues to expand our understanding of the true diversity and richness of prokaryotic genomes. Riboproteogenomics laid the foundation for dynamic studies of previously overlooked genomic elements. Most strikingly, bacterial genomes were revealed to harbor robust repertoires of small open reading frames (sORFs) encoding a diverse and broadly expressed range of small proteins, or sORF-encoded polypeptides (SEPs). In recent years, continuous efforts led to great improvements in the annotation and characterization of such proteins, yet many challenges remain to fully comprehend the pervasive nature of small proteins and their impact on bacterial biology. In this work, we review the recent developments in the dynamic field of bacterial genome reannotation, catalog the important biological roles carried out by small proteins and identify challenges obstructing the way to full understanding of these elusive proteins.
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Affiliation(s)
- Laure Simoens
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Igor Fijalkowski
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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Kohl MP, Kompatscher M, Clementi N, Holl L, Erlacher M. Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli. Nucleic Acids Res 2022; 51:271-289. [PMID: 36546769 PMCID: PMC9841429 DOI: 10.1093/nar/gkac1175] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/16/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
During initiation, the ribosome is tasked to efficiently recognize open reading frames (ORFs) for accurate and fast translation of mRNAs. A critical step is start codon recognition, which is modulated by initiation factors, mRNA structure, a Shine Dalgarno (SD) sequence and the start codon itself. Within the Escherichia coli genome, we identified more than 50 annotated initiation sites harboring AUGUG or GUGUG sequence motifs that provide two canonical start codons, AUG and GUG, in immediate proximity. As these sites may challenge start codon recognition, we studied if and how the ribosome is accurately guided to the designated ORF, with a special focus on the SD sequence as well as adenine at the fourth coding sequence position (A4). By in vitro and in vivo experiments, we characterized key requirements for unambiguous start codon recognition, but also discovered initiation sites that lead to the translation of both overlapping reading frames. Our findings corroborate the existence of an ambiguous translation initiation mechanism, implicating a multitude of so far unrecognized ORFs and translation products in bacteria.
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Affiliation(s)
- Maximilian P Kohl
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Maria Kompatscher
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Nina Clementi
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Lena Holl
- Institute of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Matthias D Erlacher
- To whom correspondence should be addressed. Tel: +43 512900370256; Fax: +43 512900373100;
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Discovery of Unannotated Small Open Reading Frames in Streptococcus pneumoniae D39 Involved in Quorum Sensing and Virulence Using Ribosome Profiling. mBio 2022; 13:e0124722. [PMID: 35852327 PMCID: PMC9426450 DOI: 10.1128/mbio.01247-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae, an opportunistic human pathogen, is the leading cause of community-acquired pneumonia and an agent of otitis media, septicemia, and meningitis. Although genomic and transcriptomic studies of S. pneumoniae have provided detailed perspectives on gene content and expression programs, they have lacked information pertaining to the translational landscape, particularly at a resolution that identifies commonly overlooked small open reading frames (sORFs), whose importance is increasingly realized in metabolism, regulation, and virulence. To identify protein-coding sORFs in S. pneumoniae, antibiotic-enhanced ribosome profiling was conducted. Using translation inhibitors, 114 novel sORFs were detected, and the expression of a subset of them was experimentally validated. Two loci associated with virulence and quorum sensing were examined in deeper detail. One such sORF, rio3, overlaps with the noncoding RNA srf-02 that was previously implicated in pathogenesis. Targeted mutagenesis parsing rio3 from srf-02 revealed that rio3 is responsible for the fitness defect seen in a murine nasopharyngeal colonization model. Additionally, two novel sORFs located adjacent to the quorum sensing receptor rgg1518 were found to impact regulatory activity. Our findings emphasize the importance of sORFs present in the genomes of pathogenic bacteria and underscore the utility of ribosome profiling for identifying the bacterial translatome.
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Kreitmeier M, Ardern Z, Abele M, Ludwig C, Scherer S, Neuhaus K. Spotlight on alternative frame coding: Two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection. iScience 2022; 25:103844. [PMID: 35198897 PMCID: PMC8850804 DOI: 10.1016/j.isci.2022.103844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/14/2021] [Accepted: 01/27/2022] [Indexed: 12/13/2022] Open
Abstract
The existence of overlapping genes (OLGs) with significant coding overlaps revolutionizes our understanding of genomic complexity. We report two exceptionally long (957 nt and 1536 nt), evolutionarily novel, translated antisense open reading frames (ORFs) embedded within annotated genes in the pathogenic Gram-negative bacterium Pseudomonas aeruginosa. Both OLG pairs show sequence features consistent with being genes and transcriptional signals in RNA sequencing. Translation of both OLGs was confirmed by ribosome profiling and mass spectrometry. Quantitative proteomics of samples taken during different phases of growth revealed regulation of protein abundances, implying biological functionality. Both OLGs are taxonomically restricted, and likely arose by overprinting within the genus. Evidence for purifying selection further supports functionality. The OLGs reported here, designated olg1 and olg2, are the longest yet proposed in prokaryotes and are among the best attested in terms of translation and evolutionary constraint. These results highlight a potentially large unexplored dimension of prokaryotic genomes. Two novel, very long, overlapping genes were found in Pseudomonas aeruginosa Both overlapping genes, olg1 and olg2, are transcribed, translated, and regulated Mass spectrometry verifies translation of the overlapping and their mother genes Both overlapping genes are taxonomically restricted, but under purifying selection
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Affiliation(s)
- Michaela Kreitmeier
- Chair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Zachary Ardern
- Chair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany.,Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Miriam Abele
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technische Universität München, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technische Universität München, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Siegfried Scherer
- Chair for Microbial Ecology, TUM School of Life Sciences, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Klaus Neuhaus
- Core Facility Microbiome, ZIEL - Institute for Food & Health, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
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Expression of the DeaD RNA helicase is regulated at multiple levels through its long mRNA 5' untranslated region. J Bacteriol 2022; 204:e0061321. [PMID: 35041499 DOI: 10.1128/jb.00613-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DEAD-box proteins (DBPs) are a prominent class of RNA remodeling proteins that alter RNA structure, a process they typically perform through an ATP-dependent RNA helicase activity. Although many DBPs have been characterized at the structural and functional level in detail, much less is known about how they are regulated. We previously showed that the messenger RNA (mRNA) for the Escherichia coli (E. coli) DeaD DBP contains an unusually long 5' untranslated region (5' UTR) of 838 nucleotides (nts) and that it is the primary RNA determinant of DeaD autoregulation. We speculated that such a long and complex 5' UTR might regulate deaD expression in additional ways. Here we show that the deaD mRNA 5' UTR regulates deaD expression at two additional levels: temperature dependent expression and through a stem-loop structure overlapping the start codon. These results support the hypothesis that a long 5' UTR can regulate gene expression through multiple mechanisms. Importance The expression of genes is frequently regulated by determinants with the 5' UTR. Although many different regulatory mechanisms that operate via the 5' UTR have been described, the functional relevance of genes with long UTRs is less clear. Here, we show that the 838 nt long 5' UTR in the deaD mRNA regulates the expression of DeaD at multiple levels. We propose that long UTRs originate to provide precise control of gene expression through multiple regulatory mechanisms, and they are indicators of the importance of their associated gene products for cellular adaptation to different environments.
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9
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Ardern Z. Small proteins: overcoming size restrictions. Nat Rev Microbiol 2021; 20:65. [PMID: 34848872 DOI: 10.1038/s41579-021-00672-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zachary Ardern
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
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