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Ranasinghe W, Gillette D, Ho A, Cho H, Choudhary M. Taxonomic Distribution, Phylogenetic Relationship, and Domain Conservation of CRISPR-Associated Cas Proteins. Bioinform Biol Insights 2024; 18:11779322241274961. [PMID: 39397878 PMCID: PMC11468465 DOI: 10.1177/11779322241274961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 07/30/2024] [Indexed: 10/15/2024] Open
Abstract
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a naturally occurring genetic defense system in bacteria and archaea. It is comprised of a series of DNA sequence repeats with spacers derived from previous exposures to plasmid or phage. Further understanding and applications of CRISPR system have revolutionized our capacity for gene or genome editing of prokaryotes and eukaryotes. The CRISPR systems are classified into 3 distinct types: type I, type II, and type III, each of which possesses an associated signature protein, Cas3, Cas9, and Cas10, respectively. As the CRISPR loci originated from earlier independent exposures of foreign genetic elements, it is likely that their associated signature proteins may have evolved rapidly. Also, their functional domain structures might have experienced different selective pressures, and therefore, they have differentially diverged in their amino acid sequences. We employed genomic, phylogenetic, and structure-function constraint analyses to reveal the evolutionary distribution, phylogenetic relationship, and structure-function constraints of Cas3, Cas9, and Cas10 proteins. Results reveal that all 3 Cas-associated proteins are highly represented in the phyla Bacteroidetes, Firmicutes, and Proteobacteria, including both pathogenic and non-pathogenic species. Genomic analysis of homologous proteins demonstrates that the proteins share 30% to 50% amino acid identity; therefore, they are low to moderately conserved and evolved rapidly. Phylogenetic analysis shows that 3 proteins originated monophyletically; however, the evolution rates were different among different branches of the clades. Furthermore, structure-function constraint analysis reveals that both Cas3 and Cas9 proteins experiences low to moderate levels of negative selection, and several protein domains of Cas3 and Cas9 proteins are highly conserved. To the contrary, most protein domains of Cas10 proteins experience neutral or positive selection, which supports rapid genetic divergence and less structure-function constraints.
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Affiliation(s)
- Weerakkody Ranasinghe
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA
| | - Dorcie Gillette
- Department of Surgery, The University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Alexis Ho
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA
| | - Hyuk Cho
- Department of Computer Science, Sam Houston State University, Huntsville, TX, USA
| | - Madhusudan Choudhary
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, USA
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Huang L, Zuo Y, Li S, Li C. Melanocyte stem cells in the skin: Origin, biological characteristics, homeostatic maintenance and therapeutic potential. Clin Transl Med 2024; 14:e1720. [PMID: 38778457 PMCID: PMC11111606 DOI: 10.1002/ctm2.1720] [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: 01/19/2024] [Revised: 05/07/2024] [Accepted: 05/12/2024] [Indexed: 05/25/2024] Open
Abstract
Melanocyte stem cells (MSCs), melanocyte lineage-specific skin stem cells derived from the neural crest, are observed in the mammalian hair follicle, the epidermis or the sweat gland. MSCs differentiate into mature melanin-producing melanocytes, which confer skin and hair pigmentation and uphold vital skin functions. In controlling and coordinating the homeostasis, repair and regeneration of skin tissue, MSCs play a vital role. Decreased numbers or impaired functions of MSCs are closely associated with the development and therapy of many skin conditions, such as hair graying, vitiligo, wound healing and melanoma. With the advancement of stem cell technology, the relevant features of MSCs have been further elaborated. In this review, we provide an exhaustive overview of cutaneous MSCs and highlight the latest advances in MSC research. A better understanding of the biological characteristics and micro-environmental regulatory mechanisms of MSCs will help to improve clinical applications in regenerative medicine, skin pigmentation disorders and cancer therapy. KEY POINTS: This review provides a concise summary of the origin, biological characteristics, homeostatic maintenance and therapeutic potential of cutaneous MSCs. The role and potential application value of MSCs in skin pigmentation disorders are discussed. The significance of single-cell RNA sequencing, CRISPR-Cas9 technology and practical models in MSCs research is highlighted.
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Affiliation(s)
- Luling Huang
- Department of DermatologyXijing HospitalFourth Military Medical UniversityXi'anChina
| | - Yuzhi Zuo
- Department of Plastic and Burns SurgeryThe Affiliated Hospital of Southwest Medical UniversityLuzhouChina
| | - Shuli Li
- Department of DermatologyXijing HospitalFourth Military Medical UniversityXi'anChina
| | - Chunying Li
- Department of DermatologyXijing HospitalFourth Military Medical UniversityXi'anChina
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Khambhati K, Bhattacharjee G, Gohil N, Dhanoa GK, Sagona AP, Mani I, Bui NL, Chu D, Karapurkar JK, Jang SH, Chung HY, Maurya R, Alzahrani KJ, Ramakrishna S, Singh V. Phage engineering and phage-assisted CRISPR-Cas delivery to combat multidrug-resistant pathogens. Bioeng Transl Med 2023; 8:e10381. [PMID: 36925687 PMCID: PMC10013820 DOI: 10.1002/btm2.10381] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/30/2022] [Accepted: 07/16/2022] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance ranks among the top threats to humanity. Due to the frequent use of antibiotics, society is facing a high prevalence of multidrug resistant pathogens, which have managed to evolve mechanisms that help them evade the last line of therapeutics. An alternative to antibiotics could involve the use of bacteriophages (phages), which are the natural predators of bacterial cells. In earlier times, phages were implemented as therapeutic agents for a century but were mainly replaced with antibiotics, and considering the menace of antimicrobial resistance, it might again become of interest due to the increasing threat of antibiotic resistance among pathogens. The current understanding of phage biology and clustered regularly interspaced short palindromic repeats (CRISPR) assisted phage genome engineering techniques have facilitated to generate phage variants with unique therapeutic values. In this review, we briefly explain strategies to engineer bacteriophages. Next, we highlight the literature supporting CRISPR-Cas9-assisted phage engineering for effective and more specific targeting of bacterial pathogens. Lastly, we discuss techniques that either help to increase the fitness, specificity, or lytic ability of bacteriophages to control an infection.
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Affiliation(s)
- Khushal Khambhati
- Department of Biosciences, School of ScienceIndrashil UniversityRajpurMehsanaGujaratIndia
| | - Gargi Bhattacharjee
- Department of Biosciences, School of ScienceIndrashil UniversityRajpurMehsanaGujaratIndia
| | - Nisarg Gohil
- Department of Biosciences, School of ScienceIndrashil UniversityRajpurMehsanaGujaratIndia
| | - Gurneet K. Dhanoa
- School of Life SciencesUniversity of Warwick, Gibbet Hill CampusCoventryUnited Kindgom
| | - Antonia P. Sagona
- School of Life SciencesUniversity of Warwick, Gibbet Hill CampusCoventryUnited Kindgom
| | - Indra Mani
- Department of MicrobiologyGargi College, University of DelhiNew DelhiIndia
| | - Nhat Le Bui
- Center for Biomedicine and Community HealthInternational School, Vietnam National UniversityHanoiVietnam
| | - Dinh‐Toi Chu
- Center for Biomedicine and Community HealthInternational School, Vietnam National UniversityHanoiVietnam
- Faculty of Applied SciencesInternational School, Vietnam National UniversityHanoiVietnam
| | | | - Su Hwa Jang
- Graduate School of Biomedical Science and EngineeringHanyang UniversitySeoulSouth Korea
- Hanyang Biomedical Research InstituteHanyang UniversitySeoulSouth Korea
| | - Hee Yong Chung
- Graduate School of Biomedical Science and EngineeringHanyang UniversitySeoulSouth Korea
- Hanyang Biomedical Research InstituteHanyang UniversitySeoulSouth Korea
- College of MedicineHanyang UniversitySeoulSouth Korea
| | - Rupesh Maurya
- Department of Biosciences, School of ScienceIndrashil UniversityRajpurMehsanaGujaratIndia
| | - Khalid J. Alzahrani
- Department of Clinical Laboratories SciencesCollege of Applied Medical Sciences, Taif UniversityTaifSaudi Arabia
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and EngineeringHanyang UniversitySeoulSouth Korea
- College of MedicineHanyang UniversitySeoulSouth Korea
| | - Vijai Singh
- Department of Biosciences, School of ScienceIndrashil UniversityRajpurMehsanaGujaratIndia
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Artificial Oocyte: Development and Potential Application. Cells 2022; 11:cells11071135. [PMID: 35406698 PMCID: PMC8998074 DOI: 10.3390/cells11071135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 02/07/2023] Open
Abstract
Millions of people around the world suffer from infertility, with the number of infertile couples and individuals increasing every year. Assisted reproductive technologies (ART) have been widely developed in recent years; however, some patients are unable to benefit from these technologies due to their lack of functional germ cells. Therefore, the development of alternative methods seems necessary. One of these methods is to create artificial oocytes. Oocytes can be generated in vitro from the ovary, fetal gonad, germline stem cells (GSCs), ovarian stem cells, or pluripotent stem cells (PSCs). This approach has raised new hopes in both basic research and medical applications. In this article, we looked at the principle of oocyte development, the landmark studies that enhanced our understanding of the cellular and molecular mechanisms that govern oogenesis in vivo, as well as the mechanisms underlying in vitro generation of functional oocytes from different sources of mouse and human stem cells. In addition, we introduced next-generation ART using somatic cells with artificial oocytes. Finally, we provided an overview of the reproductive application of in vitro oogenesis and its use in human fertility.
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Bhattacharjee G, Gohil N, Khambhati K, Mani I, Maurya R, Karapurkar JK, Gohil J, Chu DT, Vu-Thi H, Alzahrani KJ, Show PL, Rawal RM, Ramakrishna S, Singh V. Current approaches in CRISPR-Cas9 mediated gene editing for biomedical and therapeutic applications. J Control Release 2022; 343:703-723. [PMID: 35149141 DOI: 10.1016/j.jconrel.2022.02.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 12/15/2022]
Abstract
A single gene mutation can cause a number of human diseases that affect quality of life. Until the development of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) systems, it was challenging to correct a gene mutation to avoid disease by reverting phenotypes. The advent of CRISPR technology has changed the field of gene editing, given its simplicity and intrinsic programmability, surpassing the limitations of both zinc-finger nuclease and transcription activator-like effector nuclease and becoming the method of choice for therapeutic gene editing by overcoming the bottlenecks of conventional gene-editing techniques. Currently, there is no commercially available medicinal cure to correct a gene mutation that corrects and reverses the abnormality of a gene's function. Devising reprogramming strategies for faithful recapitulation of normal phenotypes is a crucial aspect for directing the reprogrammed cells toward clinical trials. The CRISPR-Cas9 system has been promising as a tool for correcting gene mutations in maladies including blood disorders and muscular degeneration as well as neurological, cardiovascular, renal, genetic, stem cell, and optical diseases. In this review, we highlight recent developments and utilization of the CRISPR-Cas9 system in correcting or generating gene mutations to create model organisms to develop deeper insights into diseases, rescue normal gene functionality, and curb the progression of a disease.
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Affiliation(s)
- Gargi Bhattacharjee
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana 382715, Gujarat, India
| | - Nisarg Gohil
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana 382715, Gujarat, India
| | - Khushal Khambhati
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana 382715, Gujarat, India
| | - Indra Mani
- Department of Microbiology, Gargi College, University of Delhi, New Delhi 110049, India
| | - Rupesh Maurya
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana 382715, Gujarat, India
| | | | - Jigresh Gohil
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana 382715, Gujarat, India
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Viet Nam
| | - Hue Vu-Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Viet Nam
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Pau-Loke Show
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, Semenyih 43500, Selangor Darul Ehsan, Malaysia
| | - Rakesh M Rawal
- Department of Biochemistry and Forensic Science, School of Sciences, Gujarat University, Ahmedabad, Gujarat 380009, India
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea; College of Medicine, Hanyang University, Seoul, South Korea.
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana 382715, Gujarat, India.
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Sidharthan DS, Abhinandan R, Balagangadharan K, Selvamurugan N. Advancements in nucleic acids-based techniques for bone regeneration. Biotechnol J 2021; 17:e2100570. [PMID: 34882984 DOI: 10.1002/biot.202100570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 12/21/2022]
Abstract
The dynamic biology of bone involving an enormous magnitude of cellular interactions and signaling transduction provides ample biomolecular targets, which can be enhanced or repressed to mediate a rapid regeneration of the impaired bone tissue. The delivery of nucleic acids such as DNA and RNA can enhance the expression of osteogenic proteins. Members of the RNA interference pathway such as miRNA and siRNA can repress negative osteoblast differentiation regulators. Advances in nanomaterials have provided researchers with a plethora of delivery modules that can ensure proper transfection. Combining the nucleic acid carrying vectors with bone scaffolds has met with tremendous success in accomplishing bone formation. Recent years have witnessed the advent of CRISPR and DNA nanostructures in regenerative medicine. This review focuses on the delivery of nucleic acids and touches upon the prospect of CRISPR and DNA nanostructures for bone tissue engineering, emphasizing their potential in treating bone defects.
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Affiliation(s)
- Dharmaraj Saleth Sidharthan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Ranganathan Abhinandan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Kalimuthu Balagangadharan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Nagarajan Selvamurugan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
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CRISPR/Cas based gene editing: marking a new era in medical science. Mol Biol Rep 2021; 48:4879-4895. [PMID: 34143395 PMCID: PMC8212587 DOI: 10.1007/s11033-021-06479-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/05/2021] [Indexed: 12/14/2022]
Abstract
CRISPR/Cas9 system, a bacterial adaptive immune system developed into a genome editing technology, has emerged as a powerful tool revolutionising genome engineering in all branches of biological science including agriculture, research and medicine. Rapid evolution of CRISPR/Cas9 system from the generation of double strand breaks to more advanced applications on gene regulation has made the wide-spread use of this technology possible. Medical science has benefited greatly from CRISPR/Cas9; being both a versatile and economical tool, it has brought gene therapy closer to reality. In this review, the development of CRISPR/Cas9 system, variants thereof and its application in different walks of medical science- research, diagnostics and therapy, will be discussed.
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