Archaea-An International Microbiological Journal最新文献

{"title":"The origin and evolution of the archaeal domain.","authors":"Gustavo Caetano-Anollés, Kyung Mo Kim","doi":"10.1155/2014/915828","DOIUrl":"https://doi.org/10.1155/2014/915828","url":null,"abstract":"With this special issue on the origin and evolution of Archaea we honor and celebrate the life and impactful contributions of Carl Woese (July 15, 1928-December 30, 2012). Carl was born and raised in Syracuse, New York. His undergraduate studies were in Amherst College and his graduate training in Yale. Sol Spiegelman brought him to the University of Illinois at Urbana-Champaign, where he unfolded a brilliant career. Carl was inspired by the originality of his mentor, Ernest C. Pollard, the tradition of biological form of D'arcy Thompson, the charisma of Francis Crick, the evolutionary tempo-mode perspective of G. G. Simpson, and the foresight of Darwin and Wallace. He understood the centrality of evolution in our understanding of biology and championed this perspective as he explored the molecular makeup of the translation machinery. His insightful mind is responsible for the discovery of the archaeal domain and for transforming comparative views of microbial diversity into an overarching evolutionary framework. Archaea constitutes the third domain of life, a remarkable group of akaryotic microbes with unique biochemical and genomic features, some of which resemble those of eukaryotes. Their habitats and lifestyles are very diverse, from extremophiles living in harsh environments to soil and marine mesophiles, from free-living microbes to gut-inhabiting methanogens and symbionts. \u0000 \u0000Carl's work did not only result in the definition of a new “urkingdom,” originally named by him as “archaebacteria,” but his insights prompted an appreciation (and respect) for the incredible microbial diversity of the biosphere. He battled the establishment to make way to a redefined microbiological science that treasured evolutionary thinking and acknowledged the centrality of microbes in the global ecosystems of our planet. He was also a harsh critic of the field of biology in general. He felt our biological views are still governed by reductionistic biases inherited from the genetic and genomic revolutions of last century, which could not identify any important questions left to answer. Furthermore, he strongly felt the biological sciences were devoted and defined by the application side, that is, by focusing on providing “service to society” through bioengineering instead of acting as “society's teacher” of man's place in the universe. A number of unsolved problems that are central to understanding life remain to be answered, and Carl posed some of the basic questions from the very beginning. What were life's origins? How did molecular and organismal complexity unfold? What are the ultimate governing principles of life? He recognized the limitations of the primacy of a genetic, molecular biology and mechanistic outlook that was gene-centered and prompted an exploration of biological complexity and emergence of biological organization within an evolutionary and physics framework. He recognized the importance of the proteinaceous backbone of life and how its desig","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2014 ","pages":"915828"},"PeriodicalIF":2.4,"publicationDate":"2014-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/915828","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32478973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Archaea: the first domain of diversified life.","authors":"Gustavo Caetano-Anollés, Arshan Nasir, Kaiyue Zhou, Derek Caetano-Anollés, Jay E Mittenthal, Feng-Jie Sun, Kyung Mo Kim","doi":"10.1155/2014/590214","DOIUrl":"10.1155/2014/590214","url":null,"abstract":"<p><p>The study of the origin of diversified life has been plagued by technical and conceptual difficulties, controversy, and apriorism. It is now popularly accepted that the universal tree of life is rooted in the akaryotes and that Archaea and Eukarya are sister groups to each other. However, evolutionary studies have overwhelmingly focused on nucleic acid and protein sequences, which partially fulfill only two of the three main steps of phylogenetic analysis, formulation of realistic evolutionary models, and optimization of tree reconstruction. In the absence of character polarization, that is, the ability to identify ancestral and derived character states, any statement about the rooting of the tree of life should be considered suspect. Here we show that macromolecular structure and a new phylogenetic framework of analysis that focuses on the parts of biological systems instead of the whole provide both deep and reliable phylogenetic signal and enable us to put forth hypotheses of origin. We review over a decade of phylogenomic studies, which mine information in a genomic census of millions of encoded proteins and RNAs. We show how the use of process models of molecular accumulation that comply with Weston's generality criterion supports a consistent phylogenomic scenario in which the origin of diversified life can be traced back to the early history of Archaea. </p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2014 ","pages":"590214"},"PeriodicalIF":2.4,"publicationDate":"2014-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4060292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32473572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The bifunctional pyruvate decarboxylase/pyruvate ferredoxin oxidoreductase from Thermococcus guaymasensis.","authors":"Mohammad S Eram,&nbsp;Erica Oduaran,&nbsp;Kesen Ma","doi":"10.1155/2014/349379","DOIUrl":"https://doi.org/10.1155/2014/349379","url":null,"abstract":"<p><p>The hyperthermophilic archaeon Thermococcus guaymasensis produces ethanol as a metabolic end product, and an alcohol dehydrogenase (ADH) catalyzing the reduction of acetaldehyde to ethanol has been purified and characterized. However, the enzyme catalyzing the formation of acetaldehyde has not been identified. In this study an enzyme catalyzing the production of acetaldehyde from pyruvate was purified and characterized from T. guaymasensis under strictly anaerobic conditions. The enzyme had both pyruvate decarboxylase (PDC) and pyruvate ferredoxin oxidoreductase (POR) activities. It was oxygen sensitive, and the optimal temperatures were 85°C and >95°C for the PDC and POR activities, respectively. The purified enzyme had activities of 3.8 ± 0.22 U mg(-1) and 20.2 ± 1.8 U mg(-1), with optimal pH-values of 9.5 and 8.4 for each activity, respectively. Coenzyme A was essential for both activities, although it did not serve as a substrate for the former. Enzyme kinetic parameters were determined separately for each activity. The purified enzyme was a heterotetramer. The sequences of the genes encoding the subunits of the bifunctional PDC/POR were determined. It is predicted that all hyperthermophilic β -keto acids ferredoxin oxidoreductases are bifunctional, catalyzing the activities of nonoxidative and oxidative decarboxylation of the corresponding β -keto acids. </p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2014 ","pages":"349379"},"PeriodicalIF":2.4,"publicationDate":"2014-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/349379","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32471363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide miRNA seeds prediction in Archaea.","authors":"Shengqin Wang,&nbsp;Yuming Xu,&nbsp;Zuhong Lu","doi":"10.1155/2014/671059","DOIUrl":"https://doi.org/10.1155/2014/671059","url":null,"abstract":"<p><p>Growing evidence indicates that miRNA genes exist in the archaeal genome, though the functional role of such noncoding RNA remains unclear. Here, we integrated the phylogenetic information of available archaeal genomes to predict miRNA seeds (typically defined as the 2-8 nucleotides of mature miRNAs) on the genomic scale. Finally, we found 2649 candidate seeds with significant conservation signal. Eleven of 29 unique seeds from previous study support our result (P value <0.01), which demonstrates that the pipeline is suitable to predict experimentally detectable miRNA seeds. The statistical significance of the overlap between the detected archaeal seeds and known eukaryotic seeds shows that the miRNA may evolve before the divergence of these two domains of cellular life. In addition, miRNA targets are enriched for genes involved in transcriptional regulation, which is consistent with the situation in eukaryote. Our research will enhance the regulatory network analysis in Archaea. </p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2014 ","pages":"671059"},"PeriodicalIF":2.4,"publicationDate":"2014-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/671059","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32441959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An antimethanogenic nutritional intervention in early life of ruminants modifies ruminal colonization by Archaea.","authors":"Leticia Abecia,&nbsp;Kate E Waddams,&nbsp;Gonzalo Martínez-Fernandez,&nbsp;A Ignacio Martín-García,&nbsp;Eva Ramos-Morales,&nbsp;C Jamie Newbold,&nbsp;David R Yáñez-Ruiz","doi":"10.1155/2014/841463","DOIUrl":"https://doi.org/10.1155/2014/841463","url":null,"abstract":"<p><p>The aim of this work was to study whether feeding a methanogen inhibitor from birth of goat kids and their does has an impact on the archaeal population colonizing the rumen and to what extent the impact persists later in life. Sixteen goats giving birth to two kids were used. Eight does were treated (D+) with bromochloromethane after giving birth and over 2 months. The other 8 goats were not treated (D-). One kid per doe in both groups was treated with bromochloromethane (k+) for 3 months while the other was untreated (k-), resulting in four experimental groups: D+/k+, D+/k-, D-/k+, and D-/k-. Rumen samples were collected from kids at weaning and 1 and 4 months after (3 and 6 months after birth) and from does at the end of the treating period (2 months). Pyrosequencing analyses showed a modified archaeal community composition colonizing the rumen of kids, although such effect did not persist entirely 4 months after; however, some less abundant groups remained different in treated and control animals. The different response on the archaeal community composition observed between offspring and adult goats suggests that the competition occurring in the developing rumen to occupy different niches offer potential for intervention. </p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2014 ","pages":"841463"},"PeriodicalIF":2.4,"publicationDate":"2014-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/841463","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32320328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diversity of the DNA replication system in the Archaea domain.","authors":"Felipe Sarmiento,&nbsp;Feng Long,&nbsp;Isaac Cann,&nbsp;William B Whitman","doi":"10.1155/2014/675946","DOIUrl":"https://doi.org/10.1155/2014/675946","url":null,"abstract":"<p><p>The precise and timely duplication of the genome is essential for cellular life. It is achieved by DNA replication, a complex process that is conserved among the three domains of life. Even though the cellular structure of archaea closely resembles that of bacteria, the information processing machinery of archaea is evolutionarily more closely related to the eukaryotic system, especially for the proteins involved in the DNA replication process. While the general DNA replication mechanism is conserved among the different domains of life, modifications in functionality and in some of the specialized replication proteins are observed. Indeed, Archaea possess specific features unique to this domain. Moreover, even though the general pattern of the replicative system is the same in all archaea, a great deal of variation exists between specific groups. </p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2014 ","pages":"675946"},"PeriodicalIF":2.4,"publicationDate":"2014-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/675946","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32310266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenetic diversity of archaea and the archaeal ammonia monooxygenase gene in uranium mining-impacted locations in Bulgaria.","authors":"Galina Radeva,&nbsp;Anelia Kenarova,&nbsp;Velina Bachvarova,&nbsp;Katrin Flemming,&nbsp;Ivan Popov,&nbsp;Dimitar Vassilev,&nbsp;Sonja Selenska-Pobell","doi":"10.1155/2014/196140","DOIUrl":"https://doi.org/10.1155/2014/196140","url":null,"abstract":"<p><p>Uranium mining and milling activities adversely affect the microbial populations of impacted sites. The negative effects of uranium on soil bacteria and fungi are well studied, but little is known about the effects of radionuclides and heavy metals on archaea. The composition and diversity of archaeal communities inhabiting the waste pile of the Sliven uranium mine and the soil of the Buhovo uranium mine were investigated using 16S rRNA gene retrieval. A total of 355 archaeal clones were selected, and their 16S rDNA inserts were analysed by restriction fragment length polymorphism (RFLP) discriminating 14 different RFLP types. All evaluated archaeal 16S rRNA gene sequences belong to the 1.1b/Nitrososphaera cluster of Crenarchaeota. The composition of the archaeal community is distinct for each site of interest and dependent on environmental characteristics, including pollution levels. Since the members of 1.1b/Nitrososphaera cluster have been implicated in the nitrogen cycle, the archaeal communities from these sites were probed for the presence of the ammonia monooxygenase gene (amoA). Our data indicate that amoA gene sequences are distributed in a similar manner as in Crenarchaeota, suggesting that archaeal nitrification processes in uranium mining-impacted locations are under the control of the same key factors controlling archaeal diversity. </p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2014 ","pages":"196140"},"PeriodicalIF":2.4,"publicationDate":"2014-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/196140","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32245001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Towards a computational model of a methane producing archaeum.","authors":"Joseph R Peterson,&nbsp;Piyush Labhsetwar,&nbsp;Jeremy R Ellermeier,&nbsp;Petra R A Kohler,&nbsp;Ankur Jain,&nbsp;Taekjip Ha,&nbsp;William W Metcalf,&nbsp;Zaida Luthey-Schulten","doi":"10.1155/2014/898453","DOIUrl":"https://doi.org/10.1155/2014/898453","url":null,"abstract":"<p><p>Progress towards a complete model of the methanogenic archaeum Methanosarcina acetivorans is reported. We characterized size distribution of the cells using differential interference contrast microscopy, finding them to be ellipsoidal with mean length and width of 2.9  μ m and 2.3  μ m, respectively, when grown on methanol and 30% smaller when grown on acetate. We used the single molecule pull down (SiMPull) technique to measure average copy number of the Mcr complex and ribosomes. A kinetic model for the methanogenesis pathways based on biochemical studies and recent metabolic reconstructions for several related methanogens is presented. In this model, 26 reactions in the methanogenesis pathways are coupled to a cell mass production reaction that updates enzyme concentrations. RNA expression data (RNA-seq) measured for cell cultures grown on acetate and methanol is used to estimate relative protein production per mole of ATP consumed. The model captures the experimentally observed methane production rates for cells growing on methanol and is most sensitive to the number of methyl-coenzyme-M reductase (Mcr) and methyl-tetrahydromethanopterin:coenzyme-M methyltransferase (Mtr) proteins. A draft transcriptional regulation network based on known interactions is proposed which we intend to integrate with the kinetic model to allow dynamic regulation. </p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2014 ","pages":"898453"},"PeriodicalIF":2.4,"publicationDate":"2014-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/898453","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32260292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Archaeal genome guardians give insights into eukaryotic DNA replication and damage response proteins.","authors":"David S Shin,&nbsp;Ashley J Pratt,&nbsp;John A Tainer","doi":"10.1155/2014/206735","DOIUrl":"https://doi.org/10.1155/2014/206735","url":null,"abstract":"<p><p>As the third domain of life, archaea, like the eukarya and bacteria, must have robust DNA replication and repair complexes to ensure genome fidelity. Archaea moreover display a breadth of unique habitats and characteristics, and structural biologists increasingly appreciate these features. As archaea include extremophiles that can withstand diverse environmental stresses, they provide fundamental systems for understanding enzymes and pathways critical to genome integrity and stress responses. Such archaeal extremophiles provide critical data on the periodic table for life as well as on the biochemical, geochemical, and physical limitations to adaptive strategies allowing organisms to thrive under environmental stress relevant to determining the boundaries for life as we know it. Specifically, archaeal enzyme structures have informed the architecture and mechanisms of key DNA repair proteins and complexes. With added abilities to temperature-trap flexible complexes and reveal core domains of transient and dynamic complexes, these structures provide insights into mechanisms of maintaining genome integrity despite extreme environmental stress. The DNA damage response protein structures noted in this review therefore inform the basis for genome integrity in the face of environmental stress, with implications for all domains of life as well as for biomanufacturing, astrobiology, and medicine. </p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2014 ","pages":"206735"},"PeriodicalIF":2.4,"publicationDate":"2014-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/206735","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32237722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of ten heterotetrameric NDP-dependent acyl-CoA synthetases of the hyperthermophilic archaeon Pyrococcus furiosus.","authors":"Joseph W Scott,&nbsp;Farris L Poole,&nbsp;Michael W W Adams","doi":"10.1155/2014/176863","DOIUrl":"https://doi.org/10.1155/2014/176863","url":null,"abstract":"<p><p>The hyperthermophilic archaeon Pyrococcus furiosus grows by fermenting peptides and carbohydrates to organic acids. In the terminal step, acyl-CoA synthetase (ACS) isoenzymes convert acyl-CoA derivatives to the corresponding acid and conserve energy in the form of ATP. ACS1 and ACS2 were previously purified from P. furiosus and have α 2 β 2 structures but the genome contains genes encoding three additional α-subunits. The ten possible combinations of α and β genes were expressed in E. coli and each resulted in stable and active α 2 β 2 isoenzymes. The α-subunit of each isoenzyme determined CoA-based substrate specificity and between them they accounted for the CoA derivatives of fourteen amino acids. The β-subunit determined preference for adenine or guanine nucleotides. The GTP-generating isoenzymes are proposed to play a role in gluconeogenesis by producing GTP for GTP-dependent phosphoenolpyruvate carboxykinase and for other GTP-dependent processes. Transcriptional and proteomic data showed that all ten isoenzymes are constitutively expressed indicating that both ATP and GTP are generated from the metabolism of most of the amino acids. A phylogenetic analysis showed that the ACSs of P. furiosus and other members of the Thermococcales are evolutionarily distinct from those found throughout the rest of biology, including those of other hyperthermophilic archaea. </p>","PeriodicalId":49105,"journal":{"name":"Archaea-An International Microbiological Journal","volume":"2014 ","pages":"176863"},"PeriodicalIF":2.4,"publicationDate":"2014-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/176863","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32209289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}