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- Constantimarinum furrinae gen. nov., sp. nov., a marine bacterium isolated from saline volcanic rock aquifer (lava seawater) at Jeju Island, Republic of Korea
- Sung-Hyun Yang , Hyun-Myung Oh , Mi-Jeong Park , Dongil Jang , Kae Kyoung Kwon
- J. Microbiol. 2022;60(1):11-17. Published online December 29, 2021
- DOI: https://doi.org/10.1007/s12275-022-1468-6
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Abstract
- A Gram-stain-negative, aerobic, rod-shaped (0.3–0.5 × 1.0– 1.9 μm), non-motile marine bacterium designated as ALE3EIT was isolated from a saline volcanic rock aquifer (lava seawater) on Jeju Island, Republic of Korea. The 16S rRNA gene sequence analysis revealed that strain ALE3EIT showed high similarity to ‘Altibacter lentus’ JLT2010T (97.2%), followed by Marixanthomonas ophiurae KMM 3046T (94.5%). Growth was observed at 10–41°C (optimum, 30°C), at pH 6.0–8.5 (optimum, pH 7.5) and at 0.5–8% (optimum, 4.0%) NaCl. The predominant cellular fatty acids were iso-C15:0 (23.5%), iso-C16:0 (10.2%), iso-C16:0 3OH (10.5%), and iso-C17:0 3OH (16.8%). The DNA G + C contents was 40.4 mol%. The major respiratory quinone was MK-6. The major polar lipids were determined to be phosphatidylethanolamine, two unidentified glycolipids, and two unidentified aminolipids. Several phenotypic characteristics such as production of acetoin, activities of arginine dihydrolase and acid phosphatase, and utilization pattern of carbon sources differentiate strain ALE3EIT from ‘A. lentus’ JLT2010T. Activities of the lipase, trypsin, α- chymotrypsin and gelatinase and utilization pattern of carbon sources differentiate strain ALE3EIT from M. ophiurae KMM 3046T. The genome of strain ALE3EIT is 3.0 Mbp long and its ANI and AAI values against ‘A. lentus’ JLT2010T were 76.58 and 72.76, respectively, however, AAI values against members in other genera were lower than 72%. The phylogenomic tree inferred by PhyloPhlAn clearly differentiated the strain ALE3EIT together with strain JLT2010T from other genera in the Falvobacteriaceae. This polyphasic taxonomic data indicates that strain ALE3EIT should be identified as a novel species in the genus ‘Altibacter’, however, the name has not been validated. Therefore, the strain is classified as a novel genus and is proposed as Constantimarinum furrinae gen. nov., sp. nov. The type strain is ALE3EIT (= KCCM 43303T = JCM 33022T).
Research Support, Non-U.S. Gov'ts
- Role of RNA Polymerase II Carboxy Terminal Domain Phosphorylation in DNA Damage Response
- Su-Jin Jeong , Hye-Jin Kim , Yong-Jin Yang , Ja-Hwan Seol , Bo-Young Jung , Jeong-Whan Han , Hyang-Woo Lee , Eun-Jung Cho
- J. Microbiol. 2005;43(6):516-522.
- DOI: https://doi.org/2296 [pii]
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Abstract
- The phosphorylation of C-terminal domain (CTD) of Rpb1p, the largest subunit of RNA polymerase II plays an important role in transcription and the coupling of various cellular events to transcription. In this study, its role in DNA damage response is closely examined in Saccharomyces cerevisiae, focusing specifically on several transcription factors that mediate or respond to the phosphorylation of the CTD. CTDK-1, the pol II CTD kinase, FCP1, the CTD phosphatase, ESS1, the CTD phosphorylation dependent cis-trans isomerase, and RSP5, the phosphorylation dependent pol II ubiquitinating enzyme, were chosen for the study. We determined that the CTD phosphorylation of CTD, which occurred predominantly at serine 2 within a heptapeptide repeat, was enhanced in response to a variety of sources of DNA damage. This modification was shown to be mediated by CTDK-1. Although mutations in ESS1 or FCP1 caused cells to become quite sensitive to DNA damage, the characteristic pattern of CTD phosphorylation remained unaltered, thereby implying that ESS1 and FCP1 play roles downstream of CTD phosphorylation in response to DNA damage. Our data suggest that the location or extent of CTD phosphorylation might be altered in response to DNA damage, and that the modified CTD, ESS1, and FCP1 all contribute to cellular survival in such conditions.
- Biochemical Quantitation of PM2 Phage DNA as a Substrate for Endonuclease Assay
- Yoo Jin Joo , Hee-Ju Kim , Jae Yung Lee , Joon Kim
- J. Microbiol. 2004;42(2):99-102.
- DOI: https://doi.org/2038 [pii]
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Abstract
- Bacteriophage PM2 has a closed circular form of double stranded DNA as a genome. This DNA from the phage is a useful source for nick-circle endonuclease assay in the fmol range. Due to difficulties in the maintenance of viral infectivity, storage conditions of the phage should be considered for the purification of PM2 DNA. The proper condition for a short-term storage of less than 2 months is to keep the PM2 phage at 4^oC; whereas the proper condition for a long-term storage of the PM2 phage for over 2 months is to keep it under liquid nitrogen in 7.5% glycerol. The optimal conditions for a high yield of phage progeny were also considered with the goal to achieve a successful PM2 DNA preparation. A MOI(Multiplicity Of Infection) of 0.03, in which the OD_600 of the host bacteria was between 0.3 and 0.5, turned out to be optimal for the mass production of PM2 phage with a burst size of about 214. Considerations of PM2 genome size, and the concentrations and radiospecific activities of purified PM2 DNA, are required to measure the endonuclease activity in the fmol range. This study reports the proper quantitation of radioactivity and the yield of purified DNA based on these conditions.
- A Novel UV-Sensitivity Mutation Induces Nucleotide Excision Repair Phenotype and Shows Epistatic Relationships with UvsF and UvsB Groups in Aspergillus nidulans
- F. Baptista , M. A. A. Castro-Prado
- J. Microbiol. 2001;39(2):102-108.
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Abstract
- DNA damage response has a central role in the maintenance of genomic integrity while mutations in related genes may result in a range of disorders, including neoplasic formations. The uvsZ1 characterized in this report is a novel uvs mutation in Aspergillus nidulans, resulting in a nucleotide excision repair (NER) phenotype: UV-sensitivity before DNA synthesis (quiescent cells), high UV-induced mutation frequency and probable absence of involvement with mitotic and meiotic recombinations. The mutation is recessive and non-allelic to the previously characterized uvsA101 mutation, also located on the paba-y interval on chromosome I. uvsZ1 showed wild-type sensitivity to MMS, which suggests non-involvement of this mutation with BER. Epitasis tests showed that the uvsZ gene product is probably involved in the same repair pathways as UVSB or UVSH proteins. Although mutations in these proteins result in an NER phenotype, UVSB is related with cell cycle control and UVSH is associated with the post-replicational repair pathway. The epistatic interaction among uvsZ1 and uvsB413 and uvsH77 mutations indicates that different repair systems may be related with the common steps of DNA damage response in Aspergillus nidulans.
- Identification and Cloning of jipA Encoding a Polypeptide That Interacts with a Homolog of Yeast Rad6, UVSJ in Aspergillus nidulans
- Jae-Han Cho^ , Seok-Soong Yun^ , Young-Kug Jang^ , Mee-Jeong Cha , Nak-Jung Kwon , Suhn-Kee Chae^
- J. Microbiol. 2003;41(1):46-51.
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Abstract
- RAD6 in yeast mediates postreplication DNA repair and is responsible for DNA-damage induced mutations. RAD6 encodes ubiquitin-conjugating enzyme that is well conserved among eukaryotic organisms. However, the molecular targets and consequences of their ubiquitination by Rad6 have remained elusive. In Aspergillus nidulans, a RAD6 homolog has been isolated and shown to be an allele of uvsJ. We screened a cDNA library to isolate UVSJ-interacting proteins by the yeast two-hybrid system. JIPA was identified as an interactor of UVSJ. Their interaction was confirmed in vitro by a GST-pull down assay. JIPA was also able to interact with mutant UVSJ proteins, UVSJ1 and the active site cysteine mutant UVSJ-C88A. The N- and the C-terminal regions of UVSJ required for the interaction with UVSH, a RAD18 homolog of yeast which physically interacts with Rad6, were not necessary for the JIPA and UVSJ interactions. About 1.4 kb jipA transcript was detected in Northern analysis and its amount was not significantly increased in response to DNA-damaging agents. A genomic DNA clone of the jipA gene was isolated from a chromosome I specific genomic library by PCR-sib selection. Sequence determination of genomic and cDNA of jipA revealed an ORF of 893 bp interrupted by 2 introns, encoding a putative polypeptide of 262 amino acids. JIPA has 33% amino acid sequence identity to TIP41 of Saccharomyces cerevisiae which negatively regulates the TOR signalling pathway.
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