Direct isolation of functional genes encoding cellulases from the microbial consortia in a thermophilic, anaerobic digester maintained on lignocellulose

1995 ◽  
Vol 43 (4) ◽  
pp. 667-674 ◽  
Author(s):  
F. G. Healy ◽  
R. M. Ray ◽  
H. C. Aldrich ◽  
A. C. Wilkie ◽  
L. O. Ingram ◽  
...  
Keyword(s):  
Anaerobic Digester ◽  
Microbial Consortia ◽  
Functional Genes ◽  
Genes Encoding

Direct isolation of functional genes encoding cellulases from the microbial consortia in a thermophilic, anaerobic digester maintained on lignocellulose

1995 ◽  
Vol 43 (4) ◽  
pp. 667-674 ◽  
Author(s):  
F. G. Healy ◽  
R. M. Ray ◽  
A. C. Wilkie ◽  
L. O. Ingram ◽  
K. T. Shanmugam ◽  
...  
Keyword(s):  
Anaerobic Digester ◽  
Microbial Consortia ◽  
Functional Genes ◽  
Genes Encoding

scholarly journals Microbial Mechanisms Mediating Increased Soil C Storage under Elevated Atmospheric N Deposition

2012 ◽  
Vol 79 (4) ◽  
pp. 1191-1199 ◽  
Author(s):  
Sarah D. Eisenlord ◽  
Zachary Freedman ◽  
Donald R. Zak ◽  
Kai Xue ◽  
Zhili He ◽  
...  
Keyword(s):  
Forest Floor ◽  
Forest Ecosystems ◽  
N Deposition ◽  
Fungal Communities ◽  
Functional Genes ◽  
Atmospheric N Deposition ◽  
Soil C ◽  
C Storage ◽  
Genes Encoding ◽  
Soil C Storage

ABSTRACTFuture rates of anthropogenic N deposition can slow the cycling and enhance the storage of C in forest ecosystems. In a northern hardwood forest ecosystem, experimental N deposition has decreased the extent of forest floor decay, leading to increased soil C storage. To better understand the microbial mechanisms mediating this response, we examined the functional genes derived from communities of actinobacteria and fungi present in the forest floor using GeoChip 4.0, a high-throughput functional-gene microarray. The compositions of functional genes derived from actinobacterial and fungal communities was significantly altered by experimental nitrogen deposition, with more heterogeneity detected in both groups. Experimental N deposition significantly decreased the richness and diversity of genes involved in the depolymerization of starch (∼12%), hemicellulose (∼16%), cellulose (∼16%), chitin (∼15%), and lignin (∼16%). The decrease in richness occurred across all taxonomic groupings detected by the microarray. The compositions of genes encoding oxidoreductases, which plausibly mediate lignin decay, were responsible for much of the observed dissimilarity between actinobacterial communities under ambient and experimental N deposition. This shift in composition and decrease in richness and diversity of genes encoding enzymes that mediate the decay process has occurred in parallel with a reduction in the extent of decay and accumulation of soil organic matter. Our observations indicate that compositional changes in actinobacterial and fungal communities elicited by experimental N deposition have functional implications for the cycling and storage of carbon in forest ecosystems.

scholarly journals The Tomato Cf-2 Disease Resistance Locus Comprises Two Functional Genes Encoding Leucine-Rich Repeat Proteins

Cell ◽  
1996 ◽  
Vol 84 (3) ◽  
pp. 451-459 ◽  
Author(s):  
Mark S Dixon ◽  
David A Jones ◽  
James S Keddie ◽  
Colwyn M Thomas ◽  
Kate Harrison ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Functional Genes ◽  
Resistance Locus ◽  
Leucine Rich Repeat ◽  
Repeat Proteins ◽  
Genes Encoding

scholarly journals Rampant prophage movement among transient competitors drives rapid adaptation during infection

2021 ◽  
Author(s):  
Christopher W. Marshall ◽  
Erin S. Gloag ◽  
Christina Lim ◽  
Daniel J. Wozniak ◽  
Vaughn S. Cooper
Keyword(s):  
Microbial Communities ◽  
Chronic Infection ◽  
Evolutionary Dynamics ◽  
Functional Genes ◽  
Rapid Adaptation ◽  
Chronic Infections ◽  
Global Regulators ◽  
New Genes ◽  
Biofilm Production ◽  
Genes Encoding

AbstractInteractions between bacteria, their close competitors, and viral parasites are common in infections but understanding of these eco-evolutionary dynamics is limited. Most examples of adaptations caused by phage lysogeny are through the acquisition of new genes. However, integrated prophages can also insert into functional genes and impart a fitness benefit by disrupting their expression, a process called active lysogeny. Here, we show that active lysogeny can fuel rapid, parallel adaptations in establishing a chronic infection. These recombination events repeatedly disrupted genes encoding global regulators, leading to increased cyclic-di-GMP levels and elevated biofilm production. The implications of prophage-mediated adaptation are broad, as even transient members of microbial communities can alter the course of evolution and generate persistent phenotypes associated with poor clinical outcomes.One Sentence SummaryBacteriophage act as genetic regulators that are key to establishing chronic infections and are rapidly shared among co-infecting strains.

scholarly journals Plastid Genome Degradation in the Endangered, Mycoheterotrophic, North American Orchid Hexalectris warnockii

2018 ◽  
Vol 10 (7) ◽  
pp. 1657-1662 ◽  
Author(s):  
Craig F Barrett ◽  
Aaron H Kennedy
Keyword(s):  
Plastid Genome ◽  
Tandem Repeats ◽  
Functional Genes ◽  
Evolutionary Models ◽  
Natural Experiments ◽  
Conservation Genetic ◽  
Genes Encoding ◽  
Plastid Genome Evolution ◽  
Plastome Degradation ◽  
Genome Degradation

Abstract Heterotrophic plants provide evolutionarily independent, natural experiments in the genomic consequences of radically altered nutritional regimes. Here, we have sequenced and annotated the plastid genome of the endangered mycoheterotrophic orchid Hexalectris warnockii. This orchid bears a plastid genome that is ∼80% the total length of the leafy, photosynthetic Phalaenopsis, and contains just over half the number of putatively functional genes of the latter. The plastid genome of H. warnockii bears pseudogenes and has experienced losses of genes encoding proteins directly (e.g., psa/psb, rbcL) and indirectly involved in photosynthesis (atp genes), suggesting it has progressed beyond the initial stages of plastome degradation, based on previous models of plastid genome evolution. Several dispersed and tandem repeats were detected, that are potentially useful as conservation genetic markers. In addition, a 29-kb inversion and a significant contraction of the inverted repeat boundaries are observed in this plastome. The Hexalectris warnockii plastid genome adds to a growing body of data useful in refining evolutionary models in parasites, and provides a resource for conservation studies in these endangered orchids.

Ribosomal protein gene regulation: what about plants?

2006 ◽  
Vol 84 (3) ◽  
pp. 342-362 ◽  
Author(s):  
Kerri B. McIntosh ◽  
Peta C. Bonham-Smith
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Ribosomal Proteins ◽  
Protein Gene ◽  
Current Knowledge ◽  
Ribosomal Protein Gene ◽  
Regulatory Mechanisms ◽  
Model Organisms ◽  
Functional Genes ◽  
Genes Encoding

The ribosome is an intricate ribonucleoprotein complex with a multitude of protein constituents present in equimolar amounts. Coordination of the synthesis of these ribosomal proteins (r-proteins) presents a major challenge to the cell. Although most r-proteins are highly conserved, the mechanisms by which r-protein gene expression is regulated often differ widely among species. While the primary regulatory mechanisms coordinating r-protein synthesis in bacteria, yeast, and animals have been identified, the mechanisms governing the coordination of plant r-protein expression remain largely unexplored. In addition, plants are unique among eukaryotes in carrying multiple (often more than two) functional genes encoding each r-protein, which substantially complicates coordinate expression. A survey of the current knowledge regarding coordinated systems of r-protein gene expression in different model organisms suggests that vertebrate r-protein gene regulation provides a valuable comparison for plants.

scholarly journals Gene drive and resilience through renewal with next generation Cleave and Rescue selfish genetic elements

2019 ◽  
Author(s):  
Georg Oberhofer ◽  
Tobin Ivy ◽  
Bruce A Hay
Keyword(s):  
Essential Gene ◽  
Functional Genes ◽  
Gene Drive ◽  
Genetic Elements ◽  
Selfish Genetic Elements ◽  
Genetic Modifications ◽  
Genes Encoding ◽  
Long Time ◽  
Beneficial Traits

AbstractGene drive-based strategies for modifying populations face the problem that genes encoding cargo and the drive mechanism are subject to separation, mutational inactivation, and loss of efficacy. Resilience, an ability to respond to these eventualities in ways that restore population modification with functional genes is needed for long-term success. Here we show that resilience can be achieved through cycles of population modification with “Cleave and Rescue” (ClvR) selfish genetic elements. ClvR comprises a DNA sequence-modifying enzyme such as Cas9/gRNAs that disrupts endogenous versions of an essential gene, and a recoded version of the essential gene resistant to cleavage. ClvR spreads by creating conditions in which those lacking ClvR die because they lack functional versions of the essential gene. Cycles of modification can in principal be carried out if two ClvR elements targeting different essential genes are located at the same genomic position, and one of them, ClvRn+1, carries a Rescue transgene from an earlier element, ClvRn. ClvRn+1 should spread within a population of ClvRn, while also bringing about a decrease in its frequency. To test this hypothesis we first show that multiple ClvRs, each targeting a different essential gene, function when located at a common chromosomal position in Drosophila. We then show that when several of these also carry the Rescue from a different ClvR, they spread to transgene fixation in populations fixed for the latter, and at its expense. Therefore, genetic modifications of populations can be overwritten with new content, providing an ongoing point of control.SignificanceGene drive can spread beneficial traits through populations, but will never be a one-shot project in which one genetic element provides all desired modifications, for an indefinitely long time. Here we show that gene drive mediated population modification in Drosophila can be overwritten with new content while eliminating old, using Cleave and Rescue (ClvR) selfish genetic elements. The ability to carry out cycles of modification that create and then leave behind a minimal genetic footprint while entering and exiting a population provides important points of control. It makes possible the replacement of broken elements, upgrades with new elements that better carry out their tasks and/or provide new functions, all while promoting the removal of modifications no longer needed.

scholarly journals Rampant prophage movement among transient competitors drives rapid adaptation during infection

2021 ◽  
Vol 7 (29) ◽  
pp. eabh1489
Author(s):  
Christopher W. Marshall ◽  
Erin S. Gloag ◽  
Christina Lim ◽  
Daniel J. Wozniak ◽  
Vaughn S. Cooper
Keyword(s):  
Microbial Communities ◽  
Clinical Outcomes ◽  
Chronic Infection ◽  
Evolutionary Dynamics ◽  
Functional Genes ◽  
Rapid Adaptation ◽  
Global Regulators ◽  
New Genes ◽  
Biofilm Production ◽  
Genes Encoding

Interactions between bacteria, their close competitors, and viral parasites are common in infections, but understanding of these eco-evolutionary dynamics is limited. Most examples of adaptations caused by phage lysogeny are through the acquisition of new genes. However, integrated prophages can also insert into functional genes and impart a fitness benefit by disrupting their expression, a process called active lysogeny. Here, we show that active lysogeny can fuel rapid, parallel adaptations in establishing a chronic infection. These recombination events repeatedly disrupted genes encoding global regulators, leading to increased cyclic di-GMP levels and elevated biofilm production. The implications of prophage-mediated adaptation are broad, as even transient members of microbial communities can alter the course of evolution and generate persistent phenotypes associated with poor clinical outcomes.

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