Extremophiles最新文献_第7页

Disorder and amino acid composition in proteins: their potential role in the adaptation of extracellular pilins to the acidic media, where Acidithiobacillus thiooxidans grows. 蛋白质中的紊乱和氨基酸组成：它们在细胞外菌毛适应酸性介质中的潜在作用，氧化硫酸硫杆菌生长在酸性介质中。

IF 2.9 3区生物学

Extremophiles Pub Date : 2023-10-17 DOI: 10.1007/s00792-023-01317-z

Edgar D Páez-Pérez, Araceli Hernández-Sánchez, Elvia Alfaro-Saldaña, J Viridiana García-Meza

{"title":"Disorder and amino acid composition in proteins: their potential role in the adaptation of extracellular pilins to the acidic media, where Acidithiobacillus thiooxidans grows.","authors":"Edgar D Páez-Pérez, Araceli Hernández-Sánchez, Elvia Alfaro-Saldaña, J Viridiana García-Meza","doi":"10.1007/s00792-023-01317-z","DOIUrl":"10.1007/s00792-023-01317-z","url":null,"abstract":"There are few biophysical studies or structural characterizations of the type IV pilin system of extremophile bacteria, such as the acidophilic Acidithiobacillus thiooxidans. We set out to analyze their pili-comprising proteins, pilins, because these extracellular proteins are in constant interaction with protons of the acidic medium in which At. thiooxidans grows. We used the web server Operon Mapper to analyze and identify the cluster codified by the minor pilin of At. thiooxidans. In addition, we carried an in-silico characterization of such pilins using the VL-XT algorithm of PONDR® server. Our results showed that structural disorder prevails more in pilins of At. thiooxidans than in non-acidophilic bacteria. Further computational characterization showed that the pilins of At. thiooxidans are significantly enriched in hydroxy (serine and threonine) and amide (glutamine and asparagine) residues, and significantly reduced in charged residues (aspartic acid, glutamic acid, arginine and lysine). Similar results were obtained when comparing pilins from other Acidithiobacillus and other acidophilic bacteria from another genus versus neutrophilic bacteria, suggesting that these properties are intrinsic to pilins from acidic environments, most likely by maintaining solubility and stability in harsh conditions. These results give guidelines for the application of extracellular proteins of acidophiles in protein engineering.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 3","pages":"31"},"PeriodicalIF":2.9,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41233752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Properties of the extracellular alkaline inulinase produced by haloalkaliphilic phototrophic bacteria Ectothiorodospirea mobilis. 嗜盐嗜碱性光营养细菌Ectothiorospirea mobili产生的胞外碱性菊粉酶的性质。

IF 2.9 3区生物学

Extremophiles Pub Date : 2023-10-17 DOI: 10.1007/s00792-023-01315-1

Levon Markosyan, Arevik Vardanyan

{"title":"Properties of the extracellular alkaline inulinase produced by haloalkaliphilic phototrophic bacteria Ectothiorodospirea mobilis.","authors":"Levon Markosyan, Arevik Vardanyan","doi":"10.1007/s00792-023-01315-1","DOIUrl":"10.1007/s00792-023-01315-1","url":null,"abstract":"The studies have revealed alkaline exoinulinase produced by haloalkaliphilic phototrophic bacteria Ectothiorhodospirea mobilis Al-2 for the first time. A new method for the isolation of a homogeneous exoinulinase from the culture broth was developed and the properties of this enzyme have been investigated. It was shown that specified exoinulinase in contrast to the studied exoinulinases produced by microorganisms exhibits catalytic activity at the wide range of pH (7.0-10) and a temperature (20-60 °C) with a maximum of the inulolitic activity at pH 9.0 and 50 °C. The studied exoinulinase possessing also invertase activity (I/S1.4) is a monomeric protein with molecular mass 57Kda, as well as Km and Vmax for inulin 3.8 mM/ml and 10 µmol/ml/min-1, respectively. The studies of the influence of different metal ions on enzyme activity have shown that Mn+2, Cu+2, Co+2, Mg+2, NaCl 5-7% promote relatively higher catalytic activity while Zn+2, Cu+2 and Fe+2 partially suppress the enzyme activity and Hg2+completely inactivates the enzyme.The formation of only fructose and glucose at the enzymatic hydrolysis of inulin confirms that the studied exoinulinase belongs to the exo-type of enzymes. The obtained results supplement our fundamental knowledge in biochemistry-enzymology, as well as the biodiversity of microorganisms expressing exoinulinase. The studied exoinulinase exhibits activity at salinity of the medium and can potentially be used in the biotechnology of inulin bioconversion into bioproducts under alkaline conditions.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 3","pages":"29"},"PeriodicalIF":2.9,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41233755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Pyrofollis japonicus gen. nov. sp. nov., a novel member of the family Pyrodictiaceae isolated from the Iheya North hydrothermal field. 日本Pyrofolis japonicus gen.nov.sp.nov.，是从伊河垭北部热液区分离得到的一个新的火管科成员。

IF 2.9 3区生物学

Extremophiles Pub Date : 2023-10-16 DOI: 10.1007/s00792-023-01316-0

Urara Miyazaki, Masaru Sanari, Akihiro Tame, Masaaki Kitajima, Akihiro Okamoto, Shigeki Sawayama, Junichi Miyazaki, Ken Takai, Satoshi Nakagawa

{"title":"Pyrofollis japonicus gen. nov. sp. nov., a novel member of the family Pyrodictiaceae isolated from the Iheya North hydrothermal field.","authors":"Urara Miyazaki, Masaru Sanari, Akihiro Tame, Masaaki Kitajima, Akihiro Okamoto, Shigeki Sawayama, Junichi Miyazaki, Ken Takai, Satoshi Nakagawa","doi":"10.1007/s00792-023-01316-0","DOIUrl":"10.1007/s00792-023-01316-0","url":null,"abstract":"A novel hyperthermophilic, heterotrophic archaeon, strain YC29T, was isolated from a deep-sea hydrothermal vent in the Mid-Okinawa Trough, Japan. Cells of strain YC29T were non-motile, irregular cocci with diameters of 1.2-3.0 µm. The strain was an obligatory fermentative anaerobe capable of growth on complex proteinaceous substrates. Growth was observed between 85 and 100 °C (optimum 90-95 °C), pH 4.9-6.4 (optimum 5.1), and in the presence of 1.4-4.0% (w/v) NaCl (optimum 3.0%). Inorganic carbon was required as a carbon source. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the family Pyrodictiaceae. The genome size was 2.02 Mbp with a G+C content of 49.4%. The maximum values for average nucleotide identity (ANI), average amino acid identity (AAI), and in silico DNA-DNA hybridization (dDDH) value of strain YC29T with relatives were 67.9% (with Pyrodictium abyssi strain AV2T), 61.1% (with Pyrodictium occultum strain PL-19T), and 33.8% (with Pyrolobus fumarii strain 1AT), respectively. Based on the phylogenetic, genomic, and phenotypic characteristics, we propose that strain YC29T represents a novel genus and species, Pyrofollis japonicus gen. nov., sp. (type strain YC29T = DSM 113394T = JCM 39171T).","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 3","pages":"28"},"PeriodicalIF":2.9,"publicationDate":"2023-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41233756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Extremophilic microbial metabolism and radioactive waste disposal. 极端微生物代谢和放射性废物处理。

IF 2.9 3区生物学

Extremophiles Pub Date : 2023-10-15 DOI: 10.1007/s00792-023-01312-4

Sarah Jane Butterworth, Franky Barton, Jonathan Richard Lloyd

{"title":"Extremophilic microbial metabolism and radioactive waste disposal.","authors":"Sarah Jane Butterworth, Franky Barton, Jonathan Richard Lloyd","doi":"10.1007/s00792-023-01312-4","DOIUrl":"10.1007/s00792-023-01312-4","url":null,"abstract":"Decades of nuclear activities have left a legacy of hazardous radioactive waste, which must be isolated from the biosphere for over 100,000 years. The preferred option for safe waste disposal is a deep subsurface geological disposal facility (GDF). Due to the very long geological timescales required, and the complexity of materials to be disposed of (including a wide range of nutrients and electron donors/acceptors) microbial activity will likely play a pivotal role in the safe operation of these mega-facilities. A GDF environment provides many metabolic challenges to microbes that may inhabit the facility, including high temperature, pressure, radiation, alkalinity, and salinity, depending on the specific disposal concept employed. However, as our understanding of the boundaries of life is continuously challenged and expanded by the discovery of novel extremophiles in Earth's most inhospitable environments, it is becoming clear that microorganisms must be considered in GDF safety cases to ensure accurate predictions of long-term performance. This review explores extremophilic adaptations and how this knowledge can be applied to challenge our current assumptions on microbial activity in GDF environments. We conclude that regardless of concept, a GDF will consist of multiple extremes and it is of high importance to understand the limits of polyextremophiles under realistic environmental conditions.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 3","pages":"27"},"PeriodicalIF":2.9,"publicationDate":"2023-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10577106/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41233753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structure/function studies of the NAD⁺-dependent DNA ligase from the poly-extremophile Deinococcus radiodurans reveal importance of the BRCT domain for DNA binding. 来自耐辐射多极端微生物Deinoccus的NAD+依赖性DNA连接酶的结构/功能研究揭示了BRCT结构域对DNA结合的重要性。

IF 2.9 3区生物学

Extremophiles Pub Date : 2023-09-15 DOI: 10.1007/s00792-023-01309-z

Andreia Fernandes, Adele Williamson, Pedro M Matias, Elin Moe

{"title":"Structure/function studies of the NAD+-dependent DNA ligase from the poly-extremophile Deinococcus radiodurans reveal importance of the BRCT domain for DNA binding.","authors":"Andreia Fernandes, Adele Williamson, Pedro M Matias, Elin Moe","doi":"10.1007/s00792-023-01309-z","DOIUrl":"10.1007/s00792-023-01309-z","url":null,"abstract":"Bacterial NAD+-dependent DNA ligases (LigAs) are enzymes involved in replication, recombination, and DNA-repair processes by catalyzing the formation of phosphodiester bonds in the backbone of DNA. These multidomain proteins exhibit four modular domains, that are highly conserved across species, with the BRCT (breast cancer type 1 C-terminus) domain on the C-terminus of the enzyme. In this study, we expressed and purified both recombinant full-length and a C-terminally truncated LigA from Deinococcus radiodurans (DrLigA and DrLigA∆BRCT) and characterized them using biochemical and X-ray crystallography techniques. Using seeds of DrLigA spherulites, we obtained ≤ 100 µm plate crystals of DrLigA∆BRCT. The crystal structure of the truncated protein was obtained at 3.4 Å resolution, revealing DrLigA∆BRCT in a non-adenylated state. Using molecular beacon-based activity assays, we demonstrated that DNA ligation via nick sealing remains unaffected in the truncated DrLigA∆BRCT. However, DNA-binding assays revealed a reduction in the affinity of DrLigA∆BRCT for dsDNA. Thus, we conclude that the flexible BRCT domain, while not critical for DNA nick-joining, plays a role in the DNA binding process, which may be a conserved function of the BRCT domain in LigA-type DNA ligases.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 3","pages":"26"},"PeriodicalIF":2.9,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10504179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10309569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genetic engineering of low-temperature polyhydroxyalkanoate production by Acidovorax sp. A1169, a psychrophile isolated from a subglacial outflow. Acidovorax sp.A1169低温生产聚羟基烷酸酯的基因工程。A1169是一种从冰下流出物中分离的嗜冷菌。

IF 2.9 3区生物学

Extremophiles Pub Date : 2023-09-14 DOI: 10.1007/s00792-023-01311-5

Jakub Grzesiak, Jan Gawor, Małgorzata Marta Rogala, Xenie Kouřilová, Stanislav Obruča

{"title":"Genetic engineering of low-temperature polyhydroxyalkanoate production by Acidovorax sp. A1169, a psychrophile isolated from a subglacial outflow.","authors":"Jakub Grzesiak, Jan Gawor, Małgorzata Marta Rogala, Xenie Kouřilová, Stanislav Obruča","doi":"10.1007/s00792-023-01311-5","DOIUrl":"10.1007/s00792-023-01311-5","url":null,"abstract":"In recent years, extremophilic microorganisms have been employed as producers of the microbial bioplastics polyhydroxyalkanoates (PHA), which are of great biotechnological value. Nevertheless, cold-loving or psychrophilic (cryophilic) bacteria have been neglected in this regard. Here, we present an investigation of the Arctic glacier-derived PHA producer Acidovorax sp. A1169. Biolog GEN III Microplates were used as a screening tool to identify the most suitable carbon substrate concerning PHA synthesis. The strain produced homopolymer poly(3-hydroxybutyrate) (PHB) most efficiently (2 g/L) at a temperature of 15 °C when supplied with fructose or mannitol as carbon sources with a substantial decrease of PHB biosynthesis at 17.5 °C. The PHB yield did not increase considerably or even decreased when carbon source concentration exceeded 10 g/L hinting that the strain is oligotrophic in nature. The strain was also capable of introducing 3-hydroxyvalerate (3HV) into the polymer structure, which is known to improve PHA thermoplastic properties. This is the first investigation providing insight into a PHA biosynthesis process by means of a true psychrophile, offering guidelines on polar-region bacteria cultivation, production of PHA and also on the methodology for genetic engineering of psychrophiles.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 3","pages":"25"},"PeriodicalIF":2.9,"publicationDate":"2023-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10501959/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10288215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Vertical segregation and phylogenetic characterization of archaea and archaeal ammonia monooxygenase gene in the water column of the western Arctic Ocean. 北冰洋西部水柱中古菌和古菌氨单加氧酶基因的垂直分离和系统发育特征。

IF 2.9 3区生物学

Extremophiles Pub Date : 2023-09-05 DOI: 10.1007/s00792-023-01310-6

Puthiya Veettil Vipindas, Thajudeen Jabir, Siddarthan Venkatachalam, Eun Jin Yang, Anand Jain, Kottekkatu Padinchati Krishnan

{"title":"Vertical segregation and phylogenetic characterization of archaea and archaeal ammonia monooxygenase gene in the water column of the western Arctic Ocean.","authors":"Puthiya Veettil Vipindas, Thajudeen Jabir, Siddarthan Venkatachalam, Eun Jin Yang, Anand Jain, Kottekkatu Padinchati Krishnan","doi":"10.1007/s00792-023-01310-6","DOIUrl":"10.1007/s00792-023-01310-6","url":null,"abstract":"Archaea constitute a substantial fraction of marine microbial biomass and play critical roles in the biogeochemistry of oceans. However, studies on their distribution and ecology in the Arctic Ocean are relatively scarce. Here, we studied the distributions of archaea and archaeal ammonia monooxygenase (amoA) gene in the western Arctic Ocean, using the amplicon sequencing approach from the sea surface to deep waters up to 3040 m depth. A total of five archaeal phyla, Nitrososphaerota, \"Euryarchaeota\", \"Halobacteriota,\" \"Nanoarchaeota\", and Candidatus Thermoplasmatota, were detected. We observed a clear, depth-dependent vertical segregation among archaeal communities. Ca. Thermoplasmatota (66.8%) was the most dominant phylum in the surface waters. At the same time, Nitrososphaerota (55.9%) was dominant in the deep waters. Most of the amoA gene OTUs (99%) belonged to the Nitrosopumilales and were further clustered into five subclades (\"NP-Alpha\", \"NP-Delta\", \"NP-Epsilon\", \"NP-Gamma\", and \"NP-Theta\"). \"NP-Epsilon\" was the most dominant clade throughout the water column and \"NP_Alpha\" showed higher abundance only in the deeper water. Salinity and inorganic nutrient concentrations were the major factors that determined the vertical segregation of archaea. We anticipate that the observed differences in the vertical distribution of archaea might contribute to the compartmentalization of dark carbon fixation and nitrification in deeper water and organic matter degradation in surface waters of the Arctic Ocean.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 3","pages":"24"},"PeriodicalIF":2.9,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10163882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Correction: Quantitative evaluation of endogenous reference genes for ddPCR under salt stress using a moderate halophile. 更正：使用中度嗜盐菌对盐胁迫下ddPCR的内源性参考基因进行定量评估。

IF 2.9 3区生物学

Extremophiles Pub Date : 2023-08-30 DOI: 10.1007/s00792-023-01307-1

Qinghua Xing, Noha M Mesbah, Haisheng Wang, Jun Li, Baisuo Zhao

引用次数: 0

The genus Anoxybacillus: an emerging and versatile source of valuable biotechnological products. 厌氧杆菌属：一种新兴的、多用途的有价值的生物技术产品来源。

IF 2.9 3区生物学

Extremophiles Pub Date : 2023-08-16 DOI: 10.1007/s00792-023-01305-3

Deisiane Fernanda da Rosa, Alexandre José Macedo

引用次数: 1

Functional expression of an antimicrobial peptide, belonging to halocin C8 family, from Natrinema sp. RNS21 in Escherichia coli. Natrinema sp.RNS21的一种属于卤代菌素C8家族的抗菌肽在大肠杆菌中的功能表达。

IF 2.9 3区生物学

Extremophiles Pub Date : 2023-08-07 DOI: 10.1007/s00792-023-01308-0

Chang Ho Ri, Song Ryong Li, Chon Il Paek, Yu Sin Kim

{"title":"Functional expression of an antimicrobial peptide, belonging to halocin C8 family, from Natrinema sp. RNS21 in Escherichia coli.","authors":"Chang Ho Ri, Song Ryong Li, Chon Il Paek, Yu Sin Kim","doi":"10.1007/s00792-023-01308-0","DOIUrl":"10.1007/s00792-023-01308-0","url":null,"abstract":"Halocins, the proteinaceous antimicrobial agents produced by haloarchaea, may be used for the preservation of salted foods and the treatment of diseases. For their application and function explanation, it is necessary to produce the active recombinants. In this work, a haloarchaeal strain producing halocin was isolated from the salt-fermented shrimp and identified as Natrinema sp. RNS21 by 16S rRNA gene sequence analysis. From 1 L of RNS21 culture, about 0.32 mg of halocin with 96% purity was obtained. Based on the molecular weight, stability and amino acid sequence alignment, the antimicrobial peptide belonged to the halocin C8 (HalC8) family. HalC8 was expressed by fusion with glutathione-S-transferase (GST) in E. coli, followed by affinity purification and enterokinase (EK) cleavage. About 6.2 mg of recombinant HalC8 with 95% purity was obtained from 1 L of E. coli culture. MALDI-TOF-MS and RP-HPLC analysis indicated that the molecular weight and folding pattern of purified recombinant HalC8 were the same as those of native HalC8. Recombinant HalC8 showed obvious inhibitory activity against Haloferax volcanii. Contrast to native HalC8, the active recombinant HalC8 could be easily produced in a short time with a high yield.","PeriodicalId":12302,"journal":{"name":"Extremophiles","volume":"27 3","pages":"21"},"PeriodicalIF":2.9,"publicationDate":"2023-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9953592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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