دورية أكاديمية
Effects of Light and Dark Conditions on the Transcriptome of Aging Cultures of Candidatus Puniceispirillum marinum IMCC1322.
| العنوان: | Effects of Light and Dark Conditions on the Transcriptome of Aging Cultures of Candidatus Puniceispirillum marinum IMCC1322. |
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| المؤلفون: | Lee JH; Department of Pediatrics, Ewha Womans University School of Medicine, Seoul, 07804, Republic of Korea., Oh HM; Institute of Liberal Arts Education, Pukyong National University, Busan, 48547, Republic of Korea. marinebio@pknu.ac.kr. |
| المصدر: | Journal of microbiology (Seoul, Korea) [J Microbiol] 2024 Apr; Vol. 62 (4), pp. 297-314. Date of Electronic Publication: 2024 Apr 25. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Microbiological Society Of Korea Country of Publication: Korea (South) NLM ID: 9703165 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1976-3794 (Electronic) Linking ISSN: 12258873 NLM ISO Abbreviation: J Microbiol Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Seoul : Microbiological Society Of Korea |
| مواضيع طبية MeSH: | Transcriptome* , Light* , Rhodopsins, Microbial*/genetics , Rhodopsins, Microbial*/metabolism , Gene Expression Regulation, Bacterial* , Darkness*, Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Gene Expression Profiling |
| مستخلص: | To elucidate the function of proteorhodopsin in Candidatus Puniceispirillum marinum strain IMCC1322, a cultivated representative of SAR116, we produced RNA-seq data under laboratory conditions. We examined the transcriptomes of six different cultures, including sets of expression changes under constant dark (DD), constant light (LL), and diel-cycled (LD; 14 h light: 10 h dark) conditions at the exponential and stationary/death phases. Prepared mRNA extracted from the six samples was analyzed on the Solexa Genome Analyzer with 36 cycles. Differentially expressed genes on the IMCC1322 genome were distinguished as four clusters by K-mean clustering and each CDS (n = 2546) was annotated based on the KEGG BRITE hierarchy. Cluster 0 (n = 1573) covered most constitutive genes including proteorhodopsin, retinoids, and glycolysis/TCA cycle. Cluster 1 genes (n = 754) were upregulated in stationary/death phase under constant dark conditions and included genes associated with bacterial defense, membrane transporters, nitrogen metabolism, and senescence signaling. Cluster 2 genes (n = 197) demonstrated upregulation in exponential phase cultures and included genes involved in genes for oxidative phosphorylation, translation factors, and transcription machinery. Cluster 3 (n = 22) contained light-stimulated upregulated genes expressed under stationary/phases. Stringent response genes belonged to cluster 2, but affected genes spanned various cellular processes such as amino acids, nucleotides, translation, transcription, glycolysis, fatty acids, and cell wall components. The coordinated expression of antagonistic stringent genes, including mazG, ppx/gppA, and spoT/relA may provide insight into the controlled cultural response observed between constant light and constant dark conditions in IMCC1322 cultures, regardless of cell numbers and biomass. (© 2024. The Author(s), under exclusive licence to Microbiological Society of Korea.) |
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| معلومات مُعتمدة: | 2018340 Korea Institute of Marine Science and Technology promotion |
| فهرسة مساهمة: | Keywords: Candidatus Puniceispirillum marinum; Exponential phase; Light; Proteorhodopsin; SAR116; Stationary/death phase; Transcriptome |
| المشرفين على المادة: | 0 (Rhodopsins, Microbial) 0 (proteorhodopsin) 0 (Bacterial Proteins) |
| تواريخ الأحداث: | Date Created: 20240425 Date Completed: 20240610 Latest Revision: 20240610 |
| رمز التحديث: | 20240610 |
| DOI: | 10.1007/s12275-024-00125-0 |
| PMID: | 38662311 |
| قاعدة البيانات: | MEDLINE |
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Full Text Finder | تدمد: | 1976-3794 |
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| DOI: | 10.1007/s12275-024-00125-0 |