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Genomics; Microbiology; Evolution; Regulation

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https://www.readbyqxmd.com/read/27687974/sar11-bacteria-the-most-abundant-plankton-in-the-oceans
#1
Stephen J Giovannoni
SAR11 is a group of small, carbon-oxidizing cells that reach a global estimated population size of 2.4 × 10(28) cells-approximately 25% of all plankton. They are found throughout the oceans but reach their largest numbers in stratified, oligotrophic gyres, which are an expanding habitat in the warming oceans. SAR11 likely had a Precambrian origin and, over geological time, evolved into the niche of harvesting labile, low-molecular-weight dissolved organic matter (DOM). SAR11 cells are minimal in size and complexity, a phenomenon known as streamlining that is thought to benefit them by lowering the material costs of replication and maximizing transport functions that are essential to competition at ultralow nutrient concentrations...
September 28, 2016: Annual Review of Marine Science
https://www.readbyqxmd.com/read/27644739/research-advances-on-microbial-genetics-in-china-in-2015
#2
Xie Jianping, Han Yubo, Liu Gang, Bai Linquan
In 2015, there are significant progresses in many aspects of the microbial genetics in China. To showcase the contribution of Chinese scientists in microbial genetics, this review surveys several notable progresses in microbial genetics made largely by Chinese scientists, and some key findings are highlighted. For the basic microbial genetics, the components, structures and functions of many macromolecule complexes involved in gene expression regulation have been elucidated. Moreover, the molecular basis underlying the recognition of foreign nucleic acids by microbial immune systems was unveiled...
September 20, 2016: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/27359215/xenogeneic-silencing-and-its-impact-on-bacterial-genomes
#3
Kamna Singh, Joshua N Milstein, William Wiley Navarre
The H-NS (heat-stable nucleoid structuring) protein affects both nucleoid compaction and global gene regulation. H-NS appears to act primarily as a silencer of AT-rich genetic material acquired by horizontal gene transfer. As such, it is key in the regulation of most genes involved in virulence and in adaptation to new environmental niches. Here we review recent progress in understanding the biochemistry of H-NS and how xenogeneic silencing affects bacterial evolution. We highlight the strengths and weaknesses of some of the models proposed in H-NS-mediated nucleoprotein complex formation...
September 8, 2016: Annual Review of Microbiology
https://www.readbyqxmd.com/read/26087620/-modern-approaches-to-the-creation-of-industrial-microorganism-strains
#4
REVIEW
V G Debabov
Microorganism producer strains are the basis of industrial biotechnology. Their properties determine the economical parameters of the production. Methods of rational design (metabolic engineering) and combinatorial methods of mutagenesis and selection (laboratory evolution, adaptive evolution, protein and genomic shuffling) are used for the construction of microorganism strains. Combination of these methods is frequently used. Modern strains usually do not contain plasmids and markers of drug resistance. All changes are introduced into the chromosome by the methods of homologous and site-specific recombination...
April 2015: Genetika
https://www.readbyqxmd.com/read/24778229/a-rifamycin-inactivating-phosphotransferase-family-shared-by-environmental-and-pathogenic-bacteria
#5
Peter Spanogiannopoulos, Nicholas Waglechner, Kalinka Koteva, Gerard D Wright
Many environmental bacteria are multidrug-resistant and represent a reservoir of ancient antibiotic resistance determinants, which have been linked to genes found in pathogens. Exploring the environmental antibiotic resistome, therefore, reveals the diversity and evolution of antibiotic resistance and also provides insight into the vulnerability of clinically used antibiotics. In this study, we describe the identification of a highly conserved regulatory motif, the rifampin (RIF) -associated element (RAE), which is found upstream of genes encoding RIF-inactivating enzymes from a diverse collection of actinomycetes...
May 13, 2014: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/24704746/crispr-cas-systems-beyond-adaptive-immunity
#6
REVIEW
Edze R Westra, Angus Buckling, Peter C Fineran
The discovery of CRISPR-Cas (clustered, regularly interspaced short palindromic repeats-CRISPR-associated proteins) adaptive immune systems in prokaryotes has been one of the most exciting advances in microbiology in the past decade. Their role in host protection against mobile genetic elements is now well established, but there is mounting evidence that these systems modulate other processes, such as the genetic regulation of group behaviour and virulence, DNA repair and genome evolution. In this Progress article, we discuss recent studies that have provided insights into these unconventional CRISPR-Cas functions and consider their potential evolutionary implications...
May 2014: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/24619102/insights-into-the-diversity-of-%C3%AF-rsm-phages-infecting-strains-of-the-phytopathogen-ralstonia-solanacearum-complex-regulation-and-evolution
#7
Ahmed Askora, Takeru Kawasaki, Makoto Fujie, Takashi Yamada
The filamentous φRSM phages (φRSM1 and φRSM3) have integration/excision capabilities in the phytopathogenic bacterium Ralstonia solanacearum. In the present study, we further investigated φRSM-like sequences present in the genomes of R. solanacearum strains belonging to the four major evolutionary lineages (phylotypes I-IV). Based on bioinformatics and comparative genomic analyses, we found that φRSM homologs are highly diverse in R. solanacearum complex strains. We detected an open reading frame (ORF)15 located upstream of the gene for φRSM integrase, which exhibited amino acid sequence similarity to phage repressor proteins...
August 2014: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/24466216/population-level-analysis-of-evolved-mutations-underlying-improvements-in-plant-hemicellulose-and-cellulose-fermentation-by-clostridium-phytofermentans
#8
Supratim Mukherjee, Lynmarie K Thompson, Stephen Godin, Wendy Schackwitz, Anna Lipzen, Joel Martin, Jeffrey L Blanchard
BACKGROUND: The complexity of plant cell walls creates many challenges for microbial decomposition. Clostridium phytofermentans, an anaerobic bacterium isolated from forest soil, directly breaks down and utilizes many plant cell wall carbohydrates. The objective of this research is to understand constraints on rates of plant decomposition by Clostridium phytofermentans and identify molecular mechanisms that may overcome these limitations. RESULTS: Experimental evolution via repeated serial transfers during exponential growth was used to select for C...
2014: PloS One
https://www.readbyqxmd.com/read/24391756/novel-insight-into-the-genetic-context-of-the-cadab-genes-from-a-4-chloro-2-methylphenoxyacetic-acid-degrading-sphingomonas
#9
Tue Kjærgaard Nielsen, Zhuofei Xu, Erkin Gözdereliler, Jens Aamand, Lars Hestbjerg Hansen, Sebastian R Sørensen
The 2-methyl-4-chlorophenoxyacetic (MCPA) acid-degrader Sphingomonas sp. ERG5 has recently been isolated from MCPA-degrading bacterial communities. Using Illumina-sequencing, the 5.7 Mb genome of this isolate was sequenced in this study, revealing the 138 kbp plasmid pCADAB1 harboring the 32.5 kbp composite transposon Tn6228 which contains genes encoding proteins for the removal of 2,4-dichlorophenoxyacetic acid (2,4-D) and MCPA, as well as the regulation of this pathway. Transposon Tn6228 was confirmed by PCR to be situated on the plasmid and also exist in a circular intermediate state - typical of IS3 elements...
2013: PloS One
https://www.readbyqxmd.com/read/24145466/the-use-of-chemostats-in-microbial-systems-biology
#10
Naomi Ziv, Nathan J Brandt, David Gresham
Cells regulate their rate of growth in response to signals from the external world. As the cell grows, diverse cellular processes must be coordinated including macromolecular synthesis, metabolism and ultimately, commitment to the cell division cycle. The chemostat, a method of experimentally controlling cell growth rate, provides a powerful means of systematically studying how growth rate impacts cellular processes - including gene expression and metabolism - and the regulatory networks that control the rate of cell growth...
2013: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/24033913/comparative-genomics-and-transcriptomics-analysis-of-experimentally-evolved-escherichia-coli-mc1000-in-complex-environments
#11
Pilar Eliana Puentes-Téllez, Ákos T Kovács, Oscar P Kuipers, Jan Dirk van Elsas
It has recently become feasible to study the basis and nature of evolutionary changes in bacteria in an experimental setting using defined media. However, assessment of adaptive changes in complex environments has been scarce. In an effort to describe the responses in such environments, we unravel, in a comparative approach, the transcriptional and genetic profiles of 19 Escherichia coli strains that evolved in Luria Bertani medium under three different oxygen regimes over 1000 generations. A positive relationship between upregulation of gene expression and the number of mutations was observed, suggesting that a number of metabolic pathways were activated...
March 2014: Environmental Microbiology
https://www.readbyqxmd.com/read/23564252/genomic-insights-into-the-fate-of-colistin-resistance-and-acinetobacter-baumannii-during-patient-treatment
#12
Evan S Snitkin, Adrian M Zelazny, Jyoti Gupta, Tara N Palmore, Patrick R Murray, Julia A Segre
Bacterial whole-genome sequencing (WGS) of human pathogens has provided unprecedented insights into the evolution of antibiotic resistance. Most studies have focused on identification of resistance mutations, leaving one to speculate on the fate of these mutants once the antibiotic selective pressure is removed. We performed WGS on longitudinal isolates of Acinetobacter baumannii from patients undergoing colistin treatment, and upon subsequent drug withdrawal. In each of the four patients, colistin resistance evolved via mutations at the pmr locus...
July 2013: Genome Research
https://www.readbyqxmd.com/read/22682889/synthetic-approaches-to-understanding-biological-constraints
#13
REVIEW
Andrea Velenich, Jeff Gore
Microbes can be readily cultured and their genomes can be easily manipulated. For these reasons, laboratory systems of unicellular organisms are increasingly used to develop and test theories about biological constraints, which manifest themselves at different levels of biological organization, from optimal gene-expression levels to complex individual and social behaviors. The quantitative description of biological constraints has recently advanced in several areas, such as the formulation of global laws governing the entire economy of a cell, the direct experimental measurement of the trade-offs leading to optimal gene expression, the description of naturally occurring fitness landscapes, and the appreciation of the requirements for a stable bacterial ecosystem...
August 2012: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/22527400/complexity-of-mirna-dependent-regulation-in-root-symbiosis
#14
REVIEW
Jérémie Bazin, Pilar Bustos-Sanmamed, Caroline Hartmann, Christine Lelandais-Brière, Martin Crespi
The development of root systems may be strongly affected by the symbiotic interactions that plants establish with soil organisms. Legumes are able to develop symbiotic relationships with both rhizobial bacteria and arbuscular mycorrhizal fungi leading to the formation of nitrogen-fixing nodules and mycorrhizal arbuscules, respectively. Both of these symbiotic interactions involve complex cellular reprogramming and profound morphological and physiological changes in specific root cells. In addition, the repression of pathogenic defence responses seems to be required for successful symbiotic interactions...
June 5, 2012: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/22493207/genome-sequence-of-a-novel-member-of-the-genus-psychrobacter-isolated-from-antarctic-soil
#15
Su Jin Kim, Seung Chul Shin, Soon Gyu Hong, Yung Mi Lee, In-Geol Choi, Hyun Park
Psychrobacter spp. have shown characteristics indicating remarkable capabilities at subzero temperatures that identify them as potential model organisms for the study of low-temperature adaptations. Here we present the draft genome sequence of Psychrobacter sp. PAMC 21119, which was isolated from permafrost soil of Antarctica; this information could provide insight into adaptation and evolution strategies under extreme environmental conditions.
May 2012: Journal of Bacteriology
https://www.readbyqxmd.com/read/22452844/complete-genome-sequence-of-bradyrhizobium-sp-s23321-insights-into-symbiosis-evolution-in-soil-oligotrophs
#16
COMPARATIVE STUDY
Takashi Okubo, Takahiro Tsukui, Hiroko Maita, Shinobu Okamoto, Kenshiro Oshima, Takatomo Fujisawa, Akihiro Saito, Hiroyuki Futamata, Reiko Hattori, Yumi Shimomura, Shin Haruta, Sho Morimoto, Yong Wang, Yoriko Sakai, Masahira Hattori, Shin-Ichi Aizawa, Kenji V P Nagashima, Sachiko Masuda, Tsutomu Hattori, Akifumi Yamashita, Zhihua Bao, Masahito Hayatsu, Hiromi Kajiya-Kanegae, Ikuo Yoshinaga, Kazunori Sakamoto, Koki Toyota, Mitsuteru Nakao, Mitsuyo Kohara, Mizue Anda, Rieko Niwa, Park Jung-Hwan, Reiko Sameshima-Saito, Shin-Ichi Tokuda, Sumiko Yamamoto, Syuji Yamamoto, Tadashi Yokoyama, Tomoko Akutsu, Yasukazu Nakamura, Yuka Nakahira-Yanaka, Yuko Takada Hoshino, Hideki Hirakawa, Hisayuki Mitsui, Kimihiro Terasawa, Manabu Itakura, Shusei Sato, Wakako Ikeda-Ohtsubo, Natsuko Sakakura, Eli Kaminuma, Kiwamu Minamisawa
Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes...
2012: Microbes and Environments
https://www.readbyqxmd.com/read/22438817/mapping-the-hsp90-genetic-interaction-network-in-candida-albicans-reveals-environmental-contingency-and-rewired-circuitry
#17
Stephanie Diezmann, Magali Michaut, Rebecca S Shapiro, Gary D Bader, Leah E Cowen
The molecular chaperone Hsp90 regulates the folding of diverse signal transducers in all eukaryotes, profoundly affecting cellular circuitry. In fungi, Hsp90 influences development, drug resistance, and evolution. Hsp90 interacts with -10% of the proteome in the model yeast Saccharomyces cerevisiae, while only two interactions have been identified in Candida albicans, the leading fungal pathogen of humans. Utilizing a chemical genomic approach, we mapped the C. albicans Hsp90 interaction network under diverse stress conditions...
2012: PLoS Genetics
https://www.readbyqxmd.com/read/22101055/heterologous-expression-and-characterization-of-two-1-hydroxy-2-naphthoic-acid-dioxygenases-from-arthrobacter-phenanthrenivorans
#18
Elpiniki Vandera, Konstantinos Kavakiotis, Aristeidis Kallimanis, Nikos C Kyrpides, Constantin Drainas, Anna-Irini Koukkou
A protein fraction exhibiting 1-hydroxy-2-naphthoic acid (1-H2NA) dioxygenase activity was purified via ion exchange, hydrophobic interactions, and gel filtration chromatography from Arthrobacter phenanthrenivorans sp. nov. strain Sphe3 isolated from a Greek creosote-oil-polluted site. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and tandem MS (MS-MS) analysis revealed that the amino acid sequences of oligopeptides of the major 45-kDa protein species, as analyzed by SDS-PAGE and silver staining, comprising 29% of the whole sequence, exhibited strong homology with 1-H2NA dioxygenase of Nocardioides sp...
February 2012: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/22041507/intrahost-passage-alters-sigb-dependent-acid-resistance-and-host-cell-associated-kinetics-of-listeria-monocytogenes
#19
Hiroshi Asakura, Keiko Kawamoto, Yumiko Okada, Fumiko Kasuga, Sou-Ichi Makino, Shigeki Yamamoto, Shizunobu Igimi
Listeria monocytogenes is a foodborne pathogen that causes gastroenteritis, maternofetal infections and meningoencephalitis in humans. Here we report that an intrahost genome mutation alters bacterial acid resistance and the abilities for replication/invasion in tissue cell culture. Among the L. monocytogenes isolates from the recent outbreak in Japan, we found that one food strain, 668, exhibited the greatest acid resistance, whereas one human clinical strain, 690, sharing identical pulsed-field gel electrophoresis (PFGE) and ribotyping patterns, exhibited an acid-sensitive phenotype...
January 2012: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/22020507/high-frequency-of-a-novel-filamentous-phage-vcy-%C3%AF-within-an-environmental-vibrio-cholerae-population
#20
Hong Xue, Yan Xu, Yan Boucher, Martin F Polz
Environmental Vibrio cholerae strains isolated from a coastal brackish pond (Oyster Pond, Woods Hole, MA) carried a novel filamentous phage, VCY, which can exist as a host genome integrative form (IF) and a plasmid-like replicative form (RF). Outside the cell, the phage displays a morphology typical of Inovirus, with filamentous particles ∼1.8 μm in length and 7 nm in width. Four independent RF isolates had identical genomes, except for 8 single nucleotide polymorphisms clustered in two regions. The overall genome size is 7,103 bp with 11 putative open reading frames organized into three functional modules (replication, structure and assembly, and regulation)...
January 2012: Applied and Environmental Microbiology
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