scholarly journals The unique coding sequence ofpmoCABoperon from type Ia methanotrophs simultaneously optimizes transcription and translation

2019 ◽  
Author(s):  
Juan C. Villada ◽  
Maria F. Duran ◽  
Patrick K. H. Lee
Keyword(s):  
Methane Oxidation ◽  
Meta Analysis ◽  
Nucleotide Composition ◽  
Global Scale ◽  
Translation Efficiency ◽  
Coding Sequences ◽  
Coding Sequence ◽  
Conserved Sequence ◽  
Type Ia ◽  
Optimal Resource

Understanding the interplay between genotype and phenotype is a fundamental goal of functional genomics. Methane oxidation is a microbial phenotype with global-scale significance as part of the carbon biogeochemical cycle, and is a sink for greenhouse gas. Microorganisms that oxidize methane (methanotrophs) are taxonomically diverse and widespread around the globe. Recent reports have suggested that type Ia methanotrophs are the most prevalent methane-oxidizing bacteria in different environments. In methanotrophic bacteria, complete methane oxidation is encoded in four operons (pmoCAB, mmoXYZBCD, mxaFI, andxoxF), but how evolution has shaped these genes to execute methane oxidation remains poorly understood. Here, we used a genomic meta-analysis to investigate the coding sequences that encode methane oxidation. By analyzing isolate and metagenome-assembled genomes from phylogenetically and geographically diverse sources, we detected an anomalous nucleotide composition bias in the coding sequences of particulate methane monooxygenase genes (pmoCAB) from type Ia methanotrophs around the globe. We found that this was a highly conserved sequence that optimizes codon usage in order to maximize translation efficiency and accuracy, while minimizing the synthesis cost of transcripts and proteins. We show that among the seven types of methanotrophs, only type Ia methanotrophs possess a unique coding sequence of thepmoCABoperon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins in environmental counter gradients with high oxygen and low methane concentrations. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence.

scholarly journals Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the pmoCAB Operon of Type Ia Methanotrophs

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Juan C. Villada ◽  
Maria F. Duran ◽  
Patrick K. H. Lee
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Methane Oxidation ◽  
Gc Content ◽  
Biogeochemical Cycle ◽  
Translation Efficiency ◽  
Coding Sequences ◽  
Different Types ◽  
Type Ia ◽  
Earth’S System

ABSTRACT Understanding the interplay between genotype and phenotype is a fundamental goal of functional genomics. Methane oxidation is a microbial phenotype with global-scale significance as part of the carbon biogeochemical cycle and a sink for greenhouse gas. Microorganisms that oxidize methane (methanotrophs) are taxonomically diverse and widespread around the globe. In methanotrophic bacteria, enzymes in the methane oxidation metabolic module (KEGG module M00174, conversion of methane to formaldehyde) are encoded in four operons (pmoCAB, mmoXYZBCD, mxaFI, and xoxF). Recent reports have suggested that methanotrophs in Proteobacteria acquired methane monooxygenases through horizontal gene transfer. Here, we used a genomic meta-analysis to infer the transcriptional and translational advantages of coding sequences from the methane oxidation metabolic modules of different types of methanotrophs. By analyzing isolate and metagenome-assembled genomes from phylogenetically and geographically diverse sources, we detected an anomalous nucleotide composition bias in the coding sequences of particulate methane monooxygenase genes (pmoCAB) from type Ia methanotrophs. We found that this nucleotide bias increases the level of codon bias by decreasing the GC content in the third base of codons, a strategy that contrasts with that of other coding sequences in the module. Further codon usage analyses uncovered that codon variants of the type Ia pmoCAB coding sequences deviate from the genomic signature to match ribosomal protein-coding sequences. Subsequently, computation of transcription and translation metrics revealed that the pmoCAB coding sequences of type Ia methanotrophs optimize the usage of codon variants to maximize translation efficiency and accuracy, while minimizing the synthesis cost of transcripts and proteins. IMPORTANCE Microbial methane oxidation plays a fundamental role in the biogeochemical cycle of Earth’s system. Recent reports have provided evidence for the acquisition of methane monooxygenases by horizontal gene transfer in methane-oxidizing bacteria from different environments, but how evolution has shaped the coding sequences to execute methanotrophy efficiently remains unexplored. In this work, we provide genomic evidence that among the different types of methanotrophs, type Ia methanotrophs possess a unique coding sequence of the pmoCAB operon that is under positive selection for optimal resource allocation and efficient synthesis of transcripts and proteins. This adaptive trait possibly enables type Ia methanotrophs to respond robustly to fluctuating methane availability and explains their global prevalence.

Conserved Subfamilies of the Drosophila HeT-A Telomere-Specific Retrotransposon

Genetics ◽  
1998 ◽  
Vol 148 (1) ◽  
pp. 233-242 ◽  
Author(s):  
Olga N Danilevskaya ◽  
Ky Lowenhaupt ◽  
Mary Lou Pardue
Keyword(s):  
Nucleotide Composition ◽  
Evolutionary Constraints ◽  
Noncoding Sequence ◽  
Strand Bias ◽  
Distinctive Pattern ◽  
Coding Sequences ◽  
Noncoding Sequences ◽  
Conserved Sequence ◽  
Dna Strand ◽  
High Level

Abstract HeT-A, a major component of Drosophila telomeres, is the first retrotransposon proposed to have a vital cellular function. Unlike most retrotransposons, more than half of its genome is noncoding. The 3′ end contains >2.5 kb of noncoding sequence. Copies of HeT-A differ by insertions or deletions and multiple nucleotide changes, which initially led us to conclude that HeT-A noncoding sequences are very fluid. However, we can now report, on the basis of new sequences and further analyses, that most of these differences are due to the existence of a small number of conserved sequence subfamilies, not to extensive sequence change during each transposition event. The high level of sequence conservation within subfamilies suggests that they arise from a small number of replicatively active elements. All HeT-A subfamilies show preservation of two intriguing features. First, segments of extremely A-rich sequence form a distinctive pattern within the 3′ noncoding region. Second, there is a strong strand bias of nucleotide composition: The DNA strand running 5′ to 3′ toward the middle of the chromosome is unusually rich in adenine and unusually poor in guanine. Although not faced with the constraints of coding sequences, the HeT-A 3′ noncoding sequence appears to be under other evolutionary constraints, possibly reflecting its roles in the telomeres.

EFFECTS of MICROPLASTICS on the FUNCTIONAL TRAITS of AQUATIC BENTHIC ORGANISMS: A GLOBAL-SCALE META-ANALYSIS

2021 ◽  
pp. 117174
Author(s):  
M. Berlino ◽  
M.C. Mangano ◽  
C. De Vittor ◽  
G. Sarà
Keyword(s):  
Functional Traits ◽  
Meta Analysis ◽  
Global Scale ◽  
Benthic Organisms

scholarly journals Comorbid Chronic Diseases and Acute Organ Injuries Are Strongly Correlated with Disease Severity and Mortality among COVID-19 Patients: A Systemic Review and Meta-Analysis

Research ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-17 ◽  
Author(s):  
Xinhui Wang ◽  
Xuexian Fang ◽  
Zhaoxian Cai ◽  
Xiaotian Wu ◽  
Xiaotong Gao ◽  
...  
Keyword(s):  
High Risk ◽  
Disease Severity ◽  
Clinical Data ◽  
Meta Analysis ◽  
Cardiac Injury ◽  
Supportive Therapy ◽  
Kidney Injury ◽  
Global Scale ◽  
Systemic Review ◽  
Increased Risk

The recent outbreak of COVID-19 has been rapidly spreading on a global scale. To date, there is no specific vaccine against the causative virus, SARS-CoV-2, nor is there an effective medicine for treating COVID-19, thus raising concerns with respect to the effect of risk factors such as clinical course and pathophysiological parameters on disease severity and outcome in patients with COVID-19. By extracting and analyzing all available published clinical data, we identified several major clinical characteristics associated with increased disease severity and mortality among patients with COVID-19. Specifically, preexisting chronic conditions such as hypertension, cardiovascular disease, chronic kidney disease, and diabetes are strongly associated with an increased risk of developing severe COVID-19; surprisingly, however, we found no correlation between chronic liver disease and increased disease severity. In addition, we found that both acute cardiac injury and acute kidney injury are highly correlated with an increased risk of COVID-19-related mortality. Given the high risk of comorbidity and the high mortality rate associated with tissue damage, organ function should be monitored closely in patients diagnosed with COVID-19, and this approach should be included when establishing new guidelines for managing these high-risk patients. Moreover, additional clinical data are needed in order to determine whether a supportive therapy can help mitigate the development of severe, potentially fatal complications, and further studies are needed to identify the pathophysiology and the mechanism underlying this novel coronavirus-associated infectious disease. Taken together, these findings provide new insights regarding clinical strategies for improving the management and outcome of patients with COVID-19.

scholarly journals A meta-analysis of global avian survival across species and latitude

2019 ◽  
Author(s):  
Micah N. Scholer ◽  
Matt Strimas-Mackey ◽  
Jill E. Jankowski
Keyword(s):  
Latitudinal Gradient ◽  
Meta Analysis ◽  
Survival Rates ◽  
Global Scale ◽  
Geographic Region ◽  
Passerine Birds ◽  
Tropical Birds ◽  
Model Predictions ◽  
Improved Model ◽  
Northern And Southern Hemispheres

AbstractTropical birds are purported to be longer lived than temperate species of similar size, but it has not been shown whether avian survival rates covary with a latitudinal gradient worldwide. Here, we perform a global-scale meta-analysis to investigate the extent of the latitudinal survival gradient. We modeled survival as a function of latitude for the separate northern and southern hemispheres, and considered phylogenetic relationships and extrinsic (climate) and intrinsic (life history) predictors hypothesized to moderate these effects. Using a database of 1,004 estimates from 246 studies of avian survival, we demonstrate that in general a latitudinal survival gradient exists in the northern hemisphere, is dampened or absent for southern hemisphere species, and that survival rates of passerine birds largely account for these trends. We found no indication that the extrinsic climate factors were better predictors of survival than latitude alone, but including species’ intrinsic traits improved model predictions. Notably, species with smaller clutch size and larger body mass showed higher survival. Our results illustrate that while some tropical birds may be longer lived than their temperate counterparts, the shape of the latitude-survival gradient differs by geographic region and is strongly influenced by species’ intrinsic traits.

scholarly journals A global comparison of grassland biomass responses to CO 2 and nitrogen enrichment

2010 ◽  
Vol 365 (1549) ◽  
pp. 2047-2056 ◽  
Author(s):  
Mark Lee ◽  
Pete Manning ◽  
Janna Rist ◽  
Sally A. Power ◽  
Charles Marsh
Keyword(s):  
Large Scale ◽  
Meta Analysis ◽  
C Sequestration ◽  
Global Scale ◽  
Scale Model ◽  
Published Data ◽  
Climate Data ◽  
Forage Production ◽  
Global Comparison ◽  
N Enrichment

Grassland ecosystems cover vast areas of the Earth's surface and provide many ecosystem services including carbon (C) storage, biodiversity preservation and the production of livestock forage. Predicting the future delivery of these services is difficult, because widespread changes in atmospheric CO 2 concentration, climate and nitrogen (N) inputs are expected. We compiled published data from global change driver manipulation experiments and combined these with climate data to assess grassland biomass responses to CO 2 and N enrichment across a range of climates. CO 2 and N enrichment generally increased aboveground biomass (AGB) but effects of CO 2 enrichment were weaker than those of N. The response to N was also dependent on the amount of N added and rainfall, with a greater response in high precipitation regions. No relationship between response to CO 2 and climate was detected within our dataset, thus suggesting that other site characteristics, e.g. soils and plant community composition, are more important regulators of grassland responses to CO 2 . A statistical model of AGB response to N was used in conjunction with projected N deposition data to estimate changes to future biomass stocks. This highlighted several potential hotspots (e.g. in some regions of China and India) of grassland AGB gain. Possible benefits for C sequestration and forage production in these regions may be offset by declines in plant biodiversity caused by these biomass gains, thus necessitating careful management if ecosystem service delivery is to be maximized. An approach such as ours, in which meta-analysis is combined with global scale model outputs to make large-scale predictions, may complement the results of dynamic global vegetation models, thus allowing us to form better predictions of biosphere responses to environmental change.

scholarly journals Global‐scale impacts of nitrogen deposition on tree carbon sequestration in tropical, temperate, and boreal forests: A meta‐analysis

2017 ◽  
Vol 24 (2) ◽  
pp. e416-e431 ◽  
Author(s):  
Lena Schulte‐Uebbing ◽  
Wim de Vries
Keyword(s):  
Carbon Sequestration ◽  
Nitrogen Deposition ◽  
Boreal Forests ◽  
Meta Analysis ◽  
Global Scale

scholarly journals Polygenic Architecture of Human Neuroanatomical Diversity

2020 ◽  
Vol 30 (4) ◽  
pp. 2307-2320
Author(s):  
Anne Biton ◽  
Nicolas Traut ◽  
Jean-Baptiste Poline ◽  
Benjamin S Aribisala ◽  
Mark E Bastin ◽  
...  
Keyword(s):  
Genetic Variance ◽  
Meta Analysis ◽  
Genetic Correlations ◽  
Global Scale ◽  
Phenotypic Variance ◽  
Environmental Correlations ◽  
Genomic Architecture ◽  
Snp Data ◽  
Environmental Causes ◽  
The Uk

Abstract We analyzed the genomic architecture of neuroanatomical diversity using magnetic resonance imaging and single nucleotide polymorphism (SNP) data from >26 000 individuals from the UK Biobank project and 5 other projects that had previously participated in the ENIGMA (Enhancing NeuroImaging Genetics through Meta-Analysis) consortium. Our results confirm the polygenic architecture of neuroanatomical diversity, with SNPs capturing from 40% to 54% of regional brain volume variance. Chromosomal length correlated with the amount of phenotypic variance captured, r ~ 0.64 on average, suggesting that at a global scale causal variants are homogeneously distributed across the genome. At a local scale, SNPs within genes (~51%) captured ~1.5 times more genetic variance than the rest, and SNPs with low minor allele frequency (MAF) captured less variance than the rest: the 40% of SNPs with MAF <5% captured <one fourth of the genetic variance. We also observed extensive pleiotropy across regions, with an average genetic correlation of rG ~ 0.45. Genetic correlations were similar to phenotypic and environmental correlations; however, genetic correlations were often larger than phenotypic correlations for the left/right volumes of the same region. The heritability of differences in left/right volumes was generally not statistically significant, suggesting an important influence of environmental causes in the variability of brain asymmetry. Our code is available athttps://github.com/neuroanatomy/genomic-architecture.

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