Journal of General and Applied Microbiology最新文献

Marine bacteria have multiple polyamide 4-degrading enzymes. 海洋细菌具有多种聚酰胺 4 降解酶。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2024-11-06 Epub Date: 2024-05-13 DOI: 10.2323/jgam.2024.05.001

Yusuke Saito, Ibuki Jin, Miwa Yamada

{"title":"Marine bacteria have multiple polyamide 4-degrading enzymes.","authors":"Yusuke Saito, Ibuki Jin, Miwa Yamada","doi":"10.2323/jgam.2024.05.001","DOIUrl":"10.2323/jgam.2024.05.001","url":null,"abstract":"Polyamide 4 (PA4) is expected to solve the issue of marine plastic pollution due to its excellent mechanical properties and biodegradability. In this study, to reveal the mechanism of PA4 biodegradation in the marine environment, we isolated 5 strains of PA4-degrading bacteria belonging to Aliiglaciecola, Dasania, and Pseudophaeobacter from a marine environment. The isolated 5 strains are novel PA4-degrading bacteria that are phylogenetically distinct from those isolated in previous studies. In addition, we compared the PA4-degrading activities and structures of the PA4-degrading enzymes secreted by the 5 strains and PA4-degrading strains isolated in our previous study. The PA4-degrading activity in the supernatant of the cultivation solutions differed among the strains. Native-PAGE and zymography using a polyacrylamide gel containing a PA4 emulsion demonstrated that PA4-degrading enzymes are classified into no less than three types of structures. These results suggested that marine PA4-degrading bacteria have multiple PA4-degrading enzymes. Our findings will contribute to a better understanding of the microbial degradation of PA4 in the marine environment.","PeriodicalId":15842,"journal":{"name":"Journal of General and Applied Microbiology","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140911066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structure of the SigF1-dependent pilA1 gene promoter and characterization of the light-activated response in the cyanobacterium Synechococcus elongatus PCC 7942. SigF1 依赖性 pilA1 基因启动子的结构和蓝藻细长球藻 PCC 7942 光激活反应的特征。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2024-11-06 Epub Date: 2024-05-20 DOI: 10.2323/jgam.2024.05.002

Ying Luo, Hitomi Imamitsu, Tatsuhiro Tsurumaki, Kan Tanaka

引用次数: 0

Directed evolution of highly sensitive and stringent choline-induced gene expression controllers. 高灵敏度和严格的胆碱诱导基因表达控制器的定向进化。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2024-11-06 Epub Date: 2024-06-17 DOI: 10.2323/jgam.2024.05.004

Yuki Yanai, Takayuki Hoshino, Yuki Kimura, Shigeko Kawai-Noma, Daisuke Umeno

{"title":"Directed evolution of highly sensitive and stringent choline-induced gene expression controllers.","authors":"Yuki Yanai, Takayuki Hoshino, Yuki Kimura, Shigeko Kawai-Noma, Daisuke Umeno","doi":"10.2323/jgam.2024.05.004","DOIUrl":"10.2323/jgam.2024.05.004","url":null,"abstract":"Gene expression controllers are useful tools for microbial production of recombinant proteins and valued bio-based chemicals. Despite its usefulness, they have rarely been applied to the practical industrial bioprocess, due to the lack of systems that meets the three requirements: low cost, safety, and tight control, to the inducer molecules. Previously, we have developed the high-spec gene induction system controlled by safe and cheap inducer choline. However, the system requires relatively high concentration (~100 mM) of choline to fully induce the gene under control. In this work, we attempted to drastically improve the sensitivity of this induction system to further reduce the induction costs. To this end, we devised a simple circuit which couples gene induction system with positive-feedback loop (P-loop) of choline importer protein BetT. After the tuning of translation level of BetT (strength of the P-loop) and deletion of endogenous betI (noise sources), highly active yet stringent control of gene expression was achieved using about 100 times less amount of inducer molecules. The choline induction system developed in this study has the lowest basal expression, the lowest choline needed to be activated, and the highest amplitude of induction as the highest available promoter such as those known as PT5 system. With this system, one can tightly control the expression level of genes of interest with negligible cost for inducer molecule, which has been the bottleneck for the application to the large-scale industrial processes.","PeriodicalId":15842,"journal":{"name":"Journal of General and Applied Microbiology","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141331105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

New insights into microorganism-derived antibiotics based on identification and antimicrobial activity of antibiotic-producing actinomycetes in kusaya gravy that lead to its high preservability. 通过鉴定草谷肉汁中产生抗生素的放线菌并确定其抗菌活性，对微生物衍生抗生素有了新的认识。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2024-11-06 Epub Date: 2024-07-31 DOI: 10.2323/jgam.2024.07.001

Sachiko Masaki, Sakura Nogimura, Takahiro Osada, Kosuke Kita, Mio Taguchi, Kana Shinoda, Ryosuke Unno, Morio Ishikawa, Toshihiro Suzuki

引用次数: 0

The chromosome level whole genome sequence and the seconary matabolism gene cluster prediction of Fusarium meridionale, the pathogen causing maize ear rot. 玉米穗腐病病原 Fusarium meridionale 的染色体水平全基因组序列和secondary matabolism 基因簇预测。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2024-11-06 Epub Date: 2024-05-28 DOI: 10.2323/jgam.2024.05.003

Qing Du, Zhaolei Tang, Juegui Su, Shichu Li

{"title":"The chromosome level whole genome sequence and the seconary matabolism gene cluster prediction of Fusarium meridionale, the pathogen causing maize ear rot.","authors":"Qing Du, Zhaolei Tang, Juegui Su, Shichu Li","doi":"10.2323/jgam.2024.05.003","DOIUrl":"10.2323/jgam.2024.05.003","url":null,"abstract":"Fusarium meridionale is one of the pathogens causing maize ear rot, it produce bioactive secondary metabolites may threaten humans food safty, however, the production mechanism of the secondary metabolites and their interaction with maize ear remains poorly understood. To facilitate related studies, we sequenced and assembled the genome of F. meridionale strain JX18-4. The size of F. meridionale JX18-4 genome is 37.11 Mbp, include four nuclear chromosome contigs that consists of 11920 coding genes and one mitochondrial contig. 95.64% gene synteny collinearity was found between the assembly and the reference genomes F. graminearum strain PH-1. Compared to the sequences of seconary matabolism gene clusters sequences reported previously, the stain JX18-4 was predicted potential producing 8 clusters, including nivalenol, zearalenone, aurofusarin, fusarielin, fusaristatin A, fusarin, fusarubin and butenolide. This study aims to reveal the molecular mechanism of secondary metabolites producing, and the genomic information of JX18-4 will provide resources for the study of biological control mechanisms and plant-microbe interactions.","PeriodicalId":15842,"journal":{"name":"Journal of General and Applied Microbiology","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141175142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rational Design of a Yeast-derived 3',5'-bisphosphate Nucleotidase with Improved Substrate Specificity. 合理设计源于酵母的 3',5'-二磷酸核苷酸酶，提高其底物特异性。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2024-11-06 Epub Date: 2024-06-18 DOI: 10.2323/jgam.2024.05.006

Jipeng Jiang, Yanqing Sun, Yanan Sun, Fuping Lu, Fufeng Liu, Huitu Zhang

{"title":"Rational Design of a Yeast-derived 3',5'-bisphosphate Nucleotidase with Improved Substrate Specificity.","authors":"Jipeng Jiang, Yanqing Sun, Yanan Sun, Fuping Lu, Fufeng Liu, Huitu Zhang","doi":"10.2323/jgam.2024.05.006","DOIUrl":"10.2323/jgam.2024.05.006","url":null,"abstract":"In recent years, a convenient phosphatase-coupled sulfotransferase assay method has been proven to be applicable to most sulfotransferases. The central principle of the method is that phosphatase specifically degrades 3'-phosphoadenosine-5'-phosphate (PAP) and leaves 3'-phosphoadenosine-5'-phosphosulfate (PAPS). Our group previously acquired a yeast 3',5'-bisphosphate nucleotidase (YND), which showed a higher catalytic activity for PAP than PAPS and could be a potential phosphatase for the sulfotransferase assay. Here, we obtained a beneficial mutant of YND with markedly improved substrate specificity towards PAP via rational design. Of 9 chosen mutation sites in the active site pocket, the mutation G236D showed the best specificity for PAP. After optimization of the reaction conditions, the mutant YNDG236D displayed a 4.8-fold increase in the catalytic ratio PAP/PAPS compared to the wild-type. We subsequently applied YNDG236D to the assay of human SULT1A1 and SULT1A3 with their known substrate 1-naphthol, indicating that the mutant could be used to evaluate sulfotransferase activity by colorimetry. Analysis of the MD simulation results revealed that the improved substrate specificity of the mutant towards PAP may stem from a more stable protein conformation and the changed flexibility of key residues in the entrance of the substrate tunnel. This research will provide a valuable reference for the development of efficient sulfotransferase activity assays.","PeriodicalId":15842,"journal":{"name":"Journal of General and Applied Microbiology","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141427003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A DUF3844 domain-containing protein is required for vacuolar protein sorting in Schizosaccharomyces pombe. 一种含 DUF3844 结构域的蛋白质是酿酒酵母菌液泡蛋白分选所必需的。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2024-10-31 DOI: 10.2323/jgam.2024.10.001

Tomoaki Inagawa, Kazuma Ohkubo, Masahiro Watanabe, Tomotake Morita, Yujiro Higuchi, Hiromi Maekawa, Kaoru Takegawa

{"title":"A DUF3844 domain-containing protein is required for vacuolar protein sorting in Schizosaccharomyces pombe.","authors":"Tomoaki Inagawa, Kazuma Ohkubo, Masahiro Watanabe, Tomotake Morita, Yujiro Higuchi, Hiromi Maekawa, Kaoru Takegawa","doi":"10.2323/jgam.2024.10.001","DOIUrl":"https://doi.org/10.2323/jgam.2024.10.001","url":null,"abstract":"Protein trafficking to vacuoles in plants and fungi, and to lysosomes in animals, is essential for the maintenance of cellular homeostasis. In Saccharomyces cerevisiae, the vacuolar protein sorting (VPS) pathway has been well studied by using vacuolar carboxypeptidase Y (CPY) as a model, and many VPS genes have been identified. By contrast, the vacuolar protein trafficking pathway in Schizosaccharomyces pombe remains poorly understood. In this study, we identified a novel VPS gene (SPBC1709.03) in S. pombe that is broadly conserved in fungi, but not in S. cerevisiae. Owing to its DUF3844 domain of unknown function, the gene was named vps3844. Disruption mutants of vps3844 had defects in both CPY sorting and incorporation of FM4-64 dye into the vacuolar membrane. Partial deletion analysis of the Vps3844 protein revealed that, within the DUF3844 domain, the region comprising amino acids 354 to 380 is important for protein trafficking to the vacuole. Our findings represent the first report of a VPS gene involved in vacuolar transport that is conserved in fungi, particularly S. pombe, but lacks representation in S. cerevisiae.","PeriodicalId":15842,"journal":{"name":"Journal of General and Applied Microbiology","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Isolation of Bacterial Endophytes Associated with Cinchona ledgeriana Moens. and Their Potential in Plant-growth Promotion, Antifungal and Quinoline Alkaloids Production. Cinchona ledgeriana Moens.的内生细菌分离及其在促进植物生长、抗真菌和生产喹啉生物碱方面的潜力。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2024-10-25 DOI: 10.2323/jgam.2024.09.002

Fauzi Akhbar Anugrah, I Nyoman Pugeg Aryantha, Rahmi Masita, Siti Zubaidah, Nur Izzati Mohd Noh

{"title":"Isolation of Bacterial Endophytes Associated with Cinchona ledgeriana Moens. and Their Potential in Plant-growth Promotion, Antifungal and Quinoline Alkaloids Production.","authors":"Fauzi Akhbar Anugrah, I Nyoman Pugeg Aryantha, Rahmi Masita, Siti Zubaidah, Nur Izzati Mohd Noh","doi":"10.2323/jgam.2024.09.002","DOIUrl":"https://doi.org/10.2323/jgam.2024.09.002","url":null,"abstract":"For centuries, quinoline alkaloids from the tree bark of Cinchona ledgeriana (C. ledgeriana) have been used in the treatment of malaria. However, unsustainable harvesting and poor growth conditions greatly limit its use as raw materials. Since plant endophytes are known to contribute to the physiology of the host and its metabolism for survival, this study showed the potential of endophytes isolated from C. ledgeriana roots in promoting the germination of Catharathus roseus (C. roseus) seedlings and the biosynthesis of quinoline alkaloid. In this present study, we found that the Enterobacteriaceae family comprised the majority of the bacterial community, with Klebsiella pneumoniae being the most abundant species at the C. ledgeriana roots. Characterization of culturable bacterial endophytes from the C. ledgeriana roots showed that all the isolates displayed plant growth-promoting factors and antifungal activities. Interestingly, chromatographic analyses led to the identification of the quinoline alkaloids producing Achromobacter xylosoxidans (A. xylosoxidans) A1. Moreover, the co-cultures of A. xylosoxidans A1, Cytobacillus solani (C. solani) A3, and Klebsiella aerogenes A6 increased the fresh and dry weight of the C. roseus seedlings. These results suggest that these bacterial endophytes may enhance quinine and quinidine production as well as the growth of the plant host.","PeriodicalId":15842,"journal":{"name":"Journal of General and Applied Microbiology","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Determination of double bond configuration of 2-hydroxy-fatty acids and emendation of cellular fatty acid composition of Aureispira marina and Aureispira maritima. 确定 2-羟基脂肪酸的双键构型并修正金鱼藻和金鱼藻的细胞脂肪酸组成。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2024-09-26 DOI: 10.2323/jgam.2024.09.001

Fuka Iriyama, Hirokazu Iida, Kazuyoshi Kawahara

{"title":"Determination of double bond configuration of 2-hydroxy-fatty acids and emendation of cellular fatty acid composition of Aureispira marina and Aureispira maritima.","authors":"Fuka Iriyama, Hirokazu Iida, Kazuyoshi Kawahara","doi":"10.2323/jgam.2024.09.001","DOIUrl":"https://doi.org/10.2323/jgam.2024.09.001","url":null,"abstract":"Aureispira marina is a marine bacterium with gliding motility isolated from the southern coastline of Thailand. It contained ceramide as a major cellular lipid composed of saturated or unsaturated branched chain 2-hydroxy-fatty acid and sphingosine. The structure of unsaturated 2-hydroxy-fatty acid was investigated in our previous study, but the geometric configuration of the double bond remained unclear. In the present study, 14-methyl-∆2-pentadecenol (∆2-iso-C16:1-ol) was prepared from D-2-hydroxy-15-methyl-∆3-hexadecenoic acid (D-2-OH-∆3-iso-C17:1) of the ceramide component, and analyzed by 1H and 13C NMR in comparison with ∆2-trans-hexadecenol (∆2-trans-n-C16:1-ol) derived from commercially available D-sphingosine. From the coupling constants of protons in the double bond and the chemical shift value of allylic carbon, the configuration of the double bond was determined as trans. Since the structure of 2-hydroxy-fatty acids was clarified, cellular fatty acids of A. marina and A. maritima, another species of the genus Aureispira, were reexamined, and the description on the cellular fatty acid composition of the genus Aureispira in the previous papers (Hosoya et al., 2006, Int. J. System. Evol. Microbiol., 56, 2931-2935; Hosoya et al., 2007, Int. J. System. Evol. Microbiol., 57, 1948-1951) lacking the description of 2-hydroxy-fatty acids was emended.","PeriodicalId":15842,"journal":{"name":"Journal of General and Applied Microbiology","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142348068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microbial community analysis of sand filters used to treat mine water from a closed uranium mine. 对用于处理封闭铀矿矿井水的砂滤器进行微生物群落分析。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2024-09-12 DOI: 10.2323/jgam.2024.08.001

Hiroshi Habe, Tomohiro Inaba, Tomo Aoyagi, Hidenobu Aizawa, Yuya Sato, Tomoyuki Hori, Keiko Yamaji, Yoshiyuki Ohara, Kenjin Fukuyama, Takuro Nishimura

{"title":"Microbial community analysis of sand filters used to treat mine water from a closed uranium mine.","authors":"Hiroshi Habe, Tomohiro Inaba, Tomo Aoyagi, Hidenobu Aizawa, Yuya Sato, Tomoyuki Hori, Keiko Yamaji, Yoshiyuki Ohara, Kenjin Fukuyama, Takuro Nishimura","doi":"10.2323/jgam.2024.08.001","DOIUrl":"https://doi.org/10.2323/jgam.2024.08.001","url":null,"abstract":"Rapid sand filters (RSFs) are employed in a drinking water treatment to remove undesirable elements such as suspended solids and dissolved metal ions. At a closed uranium (U) mine site, two sets of tandemly linked paired RSF systems (RSF1-RSF2 and RSF1-RSF3) were utilized to remove iron and manganese from mine water. In this study, a 16S rRNA-based amplicon sequencing survey was conducted to investigate the core microbes within the RSF system treating the mine water. In RSF1, two operational taxonomic units (OTUs) related to methanotrophic bacteria, Methylobacter tundripaludum (relative abundance: 18.1%) and Methylovulum psychrotolerans (11.5%), were the most and second most dominant species, respectively, alongside iron-oxidizing bacteria. The presence of these OUTs in RSF1 can be attributed to the microbial community in the inlet mine water, as the three most abundant OTUs in the mine water also dominated RSF1. Conversely, in both RSF2 and RSF3, Nevskia sp., previously isolated from the Ytterby mine manganese oxide producing ecosystem, became dominant, although known manganese-oxidizing bacterial OTUs were not detected. In contrast, a unique OTU related to Rhodanobacter sp. was the third most abundant (8.0%) in RSF1, possibly due to selective pressure from the radionuclide-contaminated environment during RSF operation, as this genus is known to be abundant at nuclear legacy waste sites. Understanding the key bacterial taxa in RSF system for mine water treatment could enhance the effectiveness of RSF processes in treating mine water from closed U mines.","PeriodicalId":15842,"journal":{"name":"Journal of General and Applied Microbiology","volume":null,"pages":null},"PeriodicalIF":0.8,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142289014","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0