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Kakouridis A, Diamond S, Eng T, Mills HJ, Gámez Holzhaus O, Summers ML, Garcia-Pichel F, Mukhopadhyay A. Desiccated Cyanobacteria Serve As Efficient Plasmid DNA Carriers in Space Flight. ACS Synth Biol 2024. [PMID: 39150229 DOI: 10.1021/acssynbio.3c00672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Effective transport of biological systems as cargo during space travel is a critical requirement to use synthetic biology and biomanufacturing in outer space. Bioproduction using microbes will drive the extent to which many human needs can be met in environments with limited resources. Vast repositories of biological parts and strains are available to meet this need, but their on-site availability requires effective transport. Here, we explore an approach that allows DNA plasmids, ubiquitous synthetic biology parts, to be safely transported to the International Space Station and back to the Kennedy Space Center without low-temperature or cryogenic stowage. Our approach relied on the cyanobacterium Nostoc punctiforme PC73102, which is naturally tolerant to prolonged desiccation. Desiccated N. punctiforme was able to carry the non-native pSCR119 plasmid as intracellular cargo safely to space and back. Upon return to the laboratory, the extracted plasmid showed no DNA damage or additional mutations and could be used as intended to transform the model synbio host Escherichia coli to bestow kanamycin resistance. This proof-of-concept study provides the foundation for a ruggedized transport host for DNA to environments where there is a need to reduce equipment and infrastructure for biological parts stowage and storage.
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Affiliation(s)
- Anne Kakouridis
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Spencer Diamond
- Innovative Genomics Institute, University of California, Berkeley, California 94720, United States
| | - Thomas Eng
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Heath J Mills
- Rhodium Scientific, Houston, Texas 77058, United States
| | | | - Michael L Summers
- Department of Biology, California State University, Northridge, California 91330, United States
| | - Ferran Garcia-Pichel
- School of Life Sciences, Arizona State University, Tempe, Arizona 85281, United States
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- School of Life Sciences, Arizona State University, Tempe, Arizona 85281, United States
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Sun Y, Guo S, Yang J, Li Y, Sun Z, Kwok LY, Sun T, Liu W, Liu W. The Space Environment Activates Capsular Polysaccharide Production in Lacticaseibacillus rhamnosus Probio-M9 by Mutating the wze ( ywqD) Gene. Microbiol Spectr 2023; 11:e0467722. [PMID: 36861974 PMCID: PMC10101077 DOI: 10.1128/spectrum.04677-22] [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: 11/16/2022] [Accepted: 02/08/2023] [Indexed: 03/03/2023] Open
Abstract
The study of microorganisms in outer space has focused mainly on investigating phenotypic changes in microbial pathogens induced by factors encountered in space. This study aimed to investigate the effect of space exposure on a probiotic bacterium, Lacticaseibacillus rhamnosus Probio-M9. Probio-M9 cells were exposed to space in a spaceflight. Interestingly, our results showed that a substantial proportion of space-exposed mutants (35/100) exhibited a ropy phenotype, characterized by their larger colony sizes and an acquired ability to produce capsular polysaccharide (CPS), compared with the original Probio-M9 or the ground control isolates without space exposure. Whole-genome sequencing analyses on both the Illumina and PacBio platforms revealed a skewed distribution of single nucleotide polymorphisms (12/89 [13.5%]) toward the CPS gene cluster, particularly in the wze (ywqD) gene. The wze gene encodes a putative tyrosine-protein kinase that regulates CPS expression through substrate phosphorylation. Transcriptomics analysis of two space-exposed ropy mutants revealed increased expression in the wze gene relative to a ground control isolate. Finally, we showed that the acquired ropy phenotype (CPS-producing ability) and space-induced genomic changes could be stably inherited. Our findings confirmed that the wze gene directly influences the capacity for CPS production in Probio-M9, and space mutagenesis is a potential strategy for inducing stable physiological changes in probiotics. IMPORTANCE This work investigated the effect of space exposure on a probiotic bacterium, Lacticaseibacillus rhamnosus Probio-M9. Interestingly, the space-exposed bacteria became capable of producing capsular polysaccharide (CPS). Some probiotic-derived CPSs have nutraceutical potential and bioactive properties. They also enhance the survival of probiotics through the gastrointestinal transit and ultimately strengthen the probiotic effects. Space mutagenesis seems to be a promising strategy for inducing stable changes in probiotics, and the obtained high-CPS-yielding mutants are valuable resources for future applications.
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Affiliation(s)
- Yue Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Shuai Guo
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Jingfang Yang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Yingmeng Li
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
- Research and Development Department, Jiangzhong Pharmaceutical Co., Ltd., Nanchang, People’s Republic of China
| | - Zhihong Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Lai-Yu Kwok
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Tiansong Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
| | - Wenjun Liu
- Research and Development Department, Jiangzhong Pharmaceutical Co., Ltd., Nanchang, People’s Republic of China
| | - Wenjun Liu
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, People’s Republic of China
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Lu C, Xu HM, Ren Q, Ao Y, Wang ZN, Ao X, Jiang L, Luo Y, Zhang X. Somatic mutation analysis of p53 and ST7 tumor suppressor genes in gastric carcinoma by DHPLC. World J Gastroenterol 2003; 9:2662-5. [PMID: 14669308 PMCID: PMC4612027 DOI: 10.3748/wjg.v9.i12.2662] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To verify the effectiveness of denaturing high-performance liquid chromatography (DHPLC) in detecting somatic mutation of p53 gene in gastric carcinoma tissues. The superiority of this method has been proved in the detection of germline mutations, but it was not very affirmative with respect to somatic mutations in tumor specimens. ST7 gene, a candidate tumor suppressor gene identified recently at human chromosome 7q31.1, was also detected because LOH at this site has also been widely reported in stomach cancer.
METHODS: DNA was extracted from 39 cases of surgical gastric carcinoma specimen and their correspondent normal mucosa. Seven fragments spanning the 11 exons were used to detect the mutation of p53 gene and the four exons reported to have mutations in ST7 gene were amplified by PCR and directly analyzed by DHPLC without mixing with wild-type allele.
RESULTS: In the analysis of p53 gene mutation, 9 aberrant DHPLC chromatographies were found in tumor tissues, while their normal-adjacent counterparts running in parallel showed a normal shape. Subsequent sequencing revealed nine sequence variations, 1 polymorphism and 8 mutations including 3 mutations not reported before. The mutation rate of p53 gene (21%) was consistent with that previously reported. Furthermore, no additional aberrant chromatography was found when wild-type DNA was added into the DNA of other 30 tumor samples that showed normal shapes previously. The positivity of p53 mutations was significantly higher in intestinal-type carcinomas (40%) than that in diffuse-type (8.33%) carcinomas of the stomach. No mutation of ST7 gene was found.
CONCLUSION: DHPLC is a very convenient method for the detection of somatic mutations in gastric carcinoma. The amount of wild type alleles supplied by the non-tumorous cells in gastric tumor specimens is enough to form heteroduplex with mutant alleles for DHPLC detection. ST7 gene may not be the target gene of inactivation at 7q31 site in gastric carcinoma.
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Affiliation(s)
- Chong Lu
- Laboratory of Medical Genomics, Oncology Department, the First Affiliated Clinical College, China Medical University, Shenyang, 110001, Liaoning Province, China
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Liu MR, Pan KF, Li ZF, Wang Y, Deng DJ, Zhang L, Lu YY. Rapid screening mitochondrial DNA mutation by using denaturing high-performance liquid chromatography. World J Gastroenterol 2002; 8:426-30. [PMID: 12046063 PMCID: PMC4656414 DOI: 10.3748/wjg.v8.i3.426] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To optimize conditions of DHPLC and analyze the effectiveness of various DNA polymerases on DHPLC resolution, and evaluate the sensitivity of DHPLC in the mutation screening of mitochondrial DNA (mtDNA).
METHODS: Two fragments of 16s gene of mitochondrial DNA (one of them F2 is a mutant fragment) and an A3243G mutated fragment were used to analyze the UV detection limit and determine the minimum percentage of mutant PCR products for DHPLC and evaluate effects of DNA polymerases on resolution of DHPLC. Under the optimal conditions, we analyzed the mtDNA mutations from muscle tissues of mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) and screened blindly for variances in D-loop region of mtDNA from human gastric tumor specimen.
RESULTS: Ten A3243G variants were detected in 12 cases of MELAS, no alterations were detected in controls and these results were consistent with the results obtained by analysis of RFLP with Apa I. We also identified 26 D-loop variances in 46 cases of human gastric cancer tissues and 38 alterations in 13 gastric cancer cell lines. The mutation of mtDNA at 80 ng PCR products containing a minimum of 5% mutant sequences could be detected by using DHPLC with UV detector. Moreover, Ampli-Taq Gold polymerase was equally as good as the proofreading DNA polymerase (e.g., Pfu) in eliminating the false positive produced by Taq DNA polymerases.
CONCLUSION: DHPLC is a powerful, rapid and sensitive mutation screening method for mtDNA. Proofreading DNA polymerase is more suitable for DHPLC analysis than Taq polymerase.
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Affiliation(s)
- Man-Ran Liu
- Beijing Institute for Cancer Research, Beijing Laboratory of Molecular Oncology, Peking University, Western District, Beijing 100034, China
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