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Li J, Wu S, Zhang K, Sun X, Lin W, Wang C, Lin S. Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects. Microorganisms 2024; 12:118. [PMID: 38257946 PMCID: PMC10820777 DOI: 10.3390/microorganisms12010118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Initially discovered over 35 years ago in the bacterium Escherichia coli as a defense system against invasion of viral (or other exogenous) DNA into the genome, CRISPR/Cas has ushered in a new era of functional genetics and served as a versatile genetic tool in all branches of life science. CRISPR/Cas has revolutionized the methodology of gene knockout with simplicity and rapidity, but it is also powerful for gene knock-in and gene modification. In the field of marine biology and ecology, this tool has been instrumental in the functional characterization of 'dark' genes and the documentation of the functional differentiation of gene paralogs. Powerful as it is, challenges exist that have hindered the advances in functional genetics in some important lineages. This review examines the status of applications of CRISPR/Cas in marine research and assesses the prospect of quickly expanding the deployment of this powerful tool to address the myriad fundamental marine biology and biological oceanography questions.
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Affiliation(s)
- Jiashun Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Shuaishuai Wu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Kaidian Zhang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Marine Biology and Fisheries, Hainan University, Haikou 570203, China
| | - Xueqiong Sun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Wenwen Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Cong Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
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Bin Hafeez A, Pełka K, Worobo R, Szweda P. In Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates. Int J Mol Sci 2024; 25:666. [PMID: 38203838 PMCID: PMC10780176 DOI: 10.3390/ijms25010666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Bacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence of virulence and antibiotic resistance properties, mobile genetic elements, and secondary metabolites. Functional annotation and Carbohydrate-Active enZYmes (CAZYme) profiling revealed the presence of genes and a repertoire of probiotics properties promoting enzymes. The isolates BB10.1, BP20.15 (isolated from bee bread), and PY2.3 (isolated from bee pollen) genome mining revealed the presence of several genes encoding acid, heat, cold, and other stress tolerance mechanisms, adhesion proteins required to survive and colonize harsh gastrointestinal environments, enzymes involved in the metabolism of dietary molecules, antioxidant activity, and genes associated with the synthesis of vitamins. In addition, genes responsible for the production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and other toxic compounds were also analyzed. Pan-genome analyses were performed with 180 Bacillus subtilis and 204 Bacillus velezensis genomes to mine for any novel genes present in the genomes of our isolates. Moreover, all three isolates also consisted of gene clusters encoding secondary metabolites.
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Affiliation(s)
- Ahmer Bin Hafeez
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| | - Karolina Pełka
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| | - Randy Worobo
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
| | - Piotr Szweda
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
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Danilova IV, Vasileva IA, Gilmutdinova AI, Dyadkina IV, Khusnullina LK, Khasanov DI, Rudakova NL, Sharipova MR. Characterization of Bacillus pumilus Strains with Targeted Gene Editing for Antimicrobial Peptides and Sporulation Factor. Microorganisms 2023; 11:1508. [PMID: 37375011 DOI: 10.3390/microorganisms11061508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/25/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Due to their capacity to produce antimicrobial peptides that can prevent the growth of diseases, many Bacillus spp. are beneficial to plants. In this study, we looked into the antagonistic activity of the B. pumilus 3-19 strain and its derivatives following targeted genome editing. Two peptide genes with antibacterial action, bacilysin (bac) and bacteriocin (bact), and the sigF gene, which encodes the sigma factor of sporulation, were specifically inactivated using the CRISPR-Cas9 system in the genome of B. pumilus 3-19. Antibacterial activity against B. cereus and Pantoea brenneri decreased as a result of the inactivation of target genes in the B. pumilus 3-19 genome, with a noticeable effect against bacilysin. The growth dynamics of the culture changed when the bac, bact, and sigF genes were inactivated, and the altered strains had less proteolytic activity. An asporogenic mutant of B. pumilus 3-19 was obtained by inactivating the sigF gene. It has been proven that bacilysin plays a unique part in the development of B. pumilus 3-19's antagonistic action against soil microorganisms.
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Affiliation(s)
- Iuliia V Danilova
- Research Laboratory "Agrobioengineering", Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Iuliia A Vasileva
- Research Laboratory "Agrobioengineering", Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Ajgul I Gilmutdinova
- Research Laboratory "Agrobioengineering", Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Ilona V Dyadkina
- Research Laboratory "Agrobioengineering", Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Liya K Khusnullina
- Research Laboratory "Agrobioengineering", Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Damir I Khasanov
- Research Laboratory "Agrobioengineering", Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Natalia L Rudakova
- Research Laboratory "Agrobioengineering", Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Margarita R Sharipova
- Research Laboratory "Agrobioengineering", Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
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Evaluation of the Marine Bacterial Population in the Great Bitter Lake, Egypt, as a Source of Antimicrobial Secondary Metabolites. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8070309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The ecological uniqueness of the Great Bitter Lake ecosystem makes its bacterial population interesting for investigation. Here, we present the first trial to evaluate the biosynthetic capacity of the bacterial population at the lake as a source of novel antimicrobials. We collected different samples from various locations throughout the lake including the oxic sediment, anoxic sediment, shore water, and off-shore water. We modified a molecular approach to compare and choose the samples with the highest bacterial biosynthetic capacity by quantifying the polyketide synthase gene clusters in their total community DNA. Furthermore, we screened the bacterial isolates recovered from these samples and their metabolic extracts for antimicrobial activity. We tried to tentatively investigate the identity of the active metabolites by PCR screening and LC–MS. The bacterial population in the oxic sediment had the highest biosynthetic capacity compared to other sample types. Four active Bacillus isolates were identified. The isolated Bacillus species were expected to produce numerous probable bioactive metabolites encoded by biosynthetic gene clusters related to the polyketide synthases (either individual or hybrid with non-ribosomal peptide synthetase), such as Bacillomycin D, Iturin A, Bacilosarcin B, Bacillcoumacin G and Macrolactin (N and G). These results suggest that the under-explored bacterial community of the Great Bitter Lake has a prospective biosynthetic capacity and can be a promising source for novel antibiotics.
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Pangenome analyses of Bacillus pumilus, Bacillus safensis, and Priestia megaterium exploring the plant-associated features of bacilli strains isolated from canola. Mol Genet Genomics 2022; 297:1063-1079. [PMID: 35612623 DOI: 10.1007/s00438-022-01907-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/05/2022] [Indexed: 12/11/2022]
Abstract
Previous genome mining of the strains Bacillus pumilus 7PB, Bacillus safensis 1TAz, 8Taz, and 32PB, and Priestia megaterium 16PB isolated from canola revealed differences in the profile of antimicrobial biosynthetic genes when compared to the species type strains. To evaluate not only the similarities among B. pumilus, B. safensis, and P. megaterium genomes but also the specificities found in the canola bacilli, we performed comparative genomic analyses through the pangenome evaluation of each species. Besides that, other genome features were explored, especially focusing on plant-associated and biotechnological characteristics. The combination of the genome metrics Average Nucleotide Identity and digital DNA-DNA hybridization formulas 1 and 3 adopting the universal thresholds of 95 and 70%, respectively, was suitable to verify the identification of strains from these groups. On average, core genes corresponded to 45%, 52%, and 34% of B. pumilus, B. safensis, and P. megaterium open pangenomes, respectively. Many genes related to adaptations to plant-associated lifestyles were predicted, especially in the Bacillus genomes. These included genes for acetoin production, polyamines utilization, root exudate chemoreceptors, biofilm formation, and plant cell-wall degrading enzymes. Overall, we could observe that strains of these species exhibit many features in common, whereas most of their variable genome portions have features yet to be uncovered. The observed antifungal activity of canola bacilli might be a result of the synergistic action of secondary metabolites, siderophores, and chitinases. Genome analysis confirmed that these species and strains have biotechnological potential to be used both as agricultural inoculants or hydrolases producers. Up to our knowledge, this is the first work that evaluates the pangenome features of P. megaterium.
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Sedeek AM, Ismail MM, Elsayed TR, Ramadan MA. Recent methods for discovering novel bioactive metabolites, specifically antimicrobial agents, from marine-associated microorganisms. Lett Appl Microbiol 2022; 75:511-525. [PMID: 35485872 DOI: 10.1111/lam.13728] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/08/2022] [Accepted: 04/19/2022] [Indexed: 12/01/2022]
Abstract
Marine microorganisms are a promising source for novel natural compounds with many medical and biotechnological applications. Here we demonstrate limitations and recent strategies for investigating the marine microbial community for novel bioactive metabolites, specifically those of antimicrobial potential. These strategies include culture-dependent methods such as modifying the standard culture media, including changing the gelling agent, dissolving vehicle, media supplementation, and preparation to access a broader range of bacterial diversity from marine samples. Furthermore, we discuss strategies like in situ cultivation, dilution-to-extinction cultivation, and long-term incubation. We are presenting recent applications of culture-independent methods such as genome mining, proteomics profiling, and the application of metagenomics as a novel strategy for structure confirmation in the discovery of the marine microorganism for novel antimicrobial metabolites. We present this review as a simple guide and a helpful resource for those who seek to enter the challenging field of applied marine microbiology.
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Affiliation(s)
- Abdelrahman M Sedeek
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismaillia, 41522, Egypt
| | - Maha M Ismail
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Tarek R Elsayed
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Egypt, Giza, 12613, Egypt
| | - Mohamed A Ramadan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
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