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Garrett SC, Philippe C, Kim JG, Wei Y, Johnson KA, Olson S, Graveley BR, Terns MP. Investigation of CRISPR-Independent Phage Resistance Mechanisms Reveals a Role for FtsH in Phage Adsorption to Streptococcus thermophilus. J Bacteriol 2023; 205:e0048222. [PMID: 37255445 PMCID: PMC10294649 DOI: 10.1128/jb.00482-22] [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: 01/06/2023] [Accepted: 05/11/2023] [Indexed: 06/01/2023] Open
Abstract
Prokaryotes are under constant pressure from phage infection and thus have evolved multiple means of defense or evasion. While CRISPR-Cas constitutes a robust immune system and appears to be the predominant means of survival for Streptococcus thermophilus when facing lytic phage infection, other forms of phage resistance coexist in this species. Here, we show that S. thermophilus strains with deleted CRISPR-Cas loci can still give rise to phage-resistant clones following lytic phage challenge. Notably, non-CRISPR phage-resistant survivors had multiple mutations which would truncate or recode a membrane-anchored host protease, FtsH. Phage adsorption was dramatically reduced in FtsH mutants, implicating this protein in phage attachment. Phages were isolated which could bypass FtsH-based resistance through mutations predicted to alter tape measure protein translation. Together, these results identify key components in phage propagation that are subject to mutation in the molecular arms race between phage and host cell. IMPORTANCE Streptococcus thermophilus is an important organism for production of cultured dairy foods, but it is susceptible to lytic phages which can lead to failed products. Consequently, mechanisms for phage resistance are an active area of research. One such mechanism is CRISPR-Cas, and S. thermophilus is a model organism for the study of this form of adaptive immunity. Here, we expand on known mechanisms with our finding that spontaneous mutations in ftsH, a gene encoding a membrane-anchored protease, protected against phage infection by disrupting phage adsorption. In turn, mutations in phage tail protein genes allowed phages to overcome ftsH-based resistance. Our results identified components in phage propagation that are subject to mutation in the molecular arms race between phage and host.
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Affiliation(s)
- Sandra C. Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Cecile Philippe
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
| | - Jenny G. Kim
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
| | - Yunzhou Wei
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
| | - Katie A. Johnson
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Brenton R. Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Michael P. Terns
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
- Department of Genetics, University of Georgia Athens, Athens, Georgia, USA
- Department of Microbiology, University of Georgia Athens, Athens, Georgia, USA
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Seedlessness Trait and Genome Editing—A Review. Int J Mol Sci 2023; 24:ijms24065660. [PMID: 36982733 PMCID: PMC10057249 DOI: 10.3390/ijms24065660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Parthenocarpy and stenospermocarpy are the two mechanisms underlying the seedless fruit set program. Seedless fruit occurs naturally and can be produced using hormone application, crossbreeding, or ploidy breeding. However, the two types of breeding are time-consuming and sometimes ineffective due to interspecies hybridization barriers or the absence of appropriate parental genotypes to use in the breeding process. The genetic engineering approach provides a better prospect, which can be explored based on an understanding of the genetic causes underlying the seedlessness trait. For instance, CRISPR/Cas is a comprehensive and precise technology. The prerequisite for using the strategy to induce seedlessness is identifying the crucial master gene or transcription factor liable for seed formation/development. In this review, we primarily explored the seedlessness mechanisms and identified the potential candidate genes underlying seed development. We also discussed the CRISPR/Cas-mediated genome editing approaches and their improvements.
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Jiang L, Yu M, Zhou Y, Tang Z, Li N, Kang J, He B, Huang J. AGONOTES: A Robot Annotator for Argonaute Proteins. Interdiscip Sci 2019; 12:109-116. [PMID: 31741225 DOI: 10.1007/s12539-019-00349-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/06/2019] [Accepted: 10/30/2019] [Indexed: 12/01/2022]
Abstract
The argonaute protein (Ago) exists in almost all organisms. In eukaryotes, it functions as a regulatory system for gene expression. In prokaryotes, it is a type of defense system against foreign invasive genomes. The Ago system has been engineered for gene silencing and genome editing and plays an important role in biological studies. With an increasing number of genomes and proteomes of various microbes becoming available, computational tools for identifying and annotating argonaute proteins are urgently needed. We introduce AGONOTES (Argonaute Notes). It is a web service especially designed for identifying and annotating Ago. AGONOTES uses the BLASTP similarity search algorithm to categorize all submitted proteins into three groups: prokaryotic argonaute protein (pAgo), eukaryotic argonaute protein (eAgo), and non-argonaute protein (non-Ago). Argonaute proteins can then be aligned to the corresponding standard set of Ago sequences using the multiple sequence alignment program MUSCLE. All functional domains of Ago can further be curated from the alignment results and visualized easily through Bio::Graphic modules in the BioPerl bundle. Compared with existing tools such as CD-Search and available databases such as UniProt and AGONOTES showed a much better performance on domain annotations, which is fundamental in studying the new Ago. AGONOTES can be freely accessed at http://i.uestc.edu.cn/agonotes/. AGONOTES is a friendly tool for annotating Ago domains from a proteome or a series of protein sequences.
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Affiliation(s)
- Lixu Jiang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China
| | - Min Yu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China
| | - Yuwei Zhou
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China
| | - Zhongjie Tang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China
| | - Ning Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China
| | - Juanjuan Kang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China
| | - Bifang He
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China.,School of Medicine, Guizhou University, Guiyang, China
| | - Jian Huang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China.
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Mahmoudian-sani MR, Farnoosh G, Mahdavinezhad A, Saidijam M. CRISPR genome editing and its medical applications. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1406823] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Mohammad-Reza Mahmoudian-sani
- Laboratory of Molecular Biology, Department of Genetics and Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Gholamreza Farnoosh
- Nanobiotechnology Laboratory, Department of Medical Biotechnology, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Mahdavinezhad
- Laboratory of Molecular Biology, Department of Genetics and Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Massoud Saidijam
- Laboratory of Molecular Biology, Department of Genetics and Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
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Dai X, Chen X, Fang Q, Li J, Bai Z. Inducible CRISPR genome-editing tool: classifications and future trends. Crit Rev Biotechnol 2017; 38:573-586. [DOI: 10.1080/07388551.2017.1378999] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xiaofeng Dai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiao Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Qiuwu Fang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jia Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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