scholarly journals Janthinobacterium CG23_2: Comparative Genome Analysis Reveals Enhanced Environmental Sensing and Transcriptional Regulation for Adaptation to Life in an Antarctic Supraglacial Stream

2019 ◽  
Vol 7 (10) ◽  
pp. 454
Author(s):  
Markus Dieser ◽  
Heidi J. Smith ◽  
Thiruvarangan Ramaraj ◽  
Christine M. Foreman
Keyword(s):  
Transcriptional Regulation ◽  
Extreme Environment ◽  
Ecological Niches ◽  
Genome Plasticity ◽  
Functional Categories ◽  
Environmental Sensing ◽  
Copy Numbers ◽  
Environmental Extremes ◽  
Species Specific ◽  
Extracellular Environment

As many bacteria detected in Antarctic environments are neither true psychrophiles nor endemic species, their proliferation in spite of environmental extremes gives rise to genome adaptations. Janthinobacterium sp. CG23_2 is a bacterial isolate from the Cotton Glacier stream, Antarctica. To understand how Janthinobacterium sp. CG23_2 has adapted to its environment, we investigated its genomic traits in comparison to genomes of 35 published Janthinobacterium species. While we hypothesized that genome shrinkage and specialization to narrow ecological niches would be energetically favorable for dwelling in an ephemeral Antarctic stream, the genome of Janthinobacterium sp. CG23_2 was on average 1.7 ± 0.6 Mb larger and predicted 1411 ± 499 more coding sequences compared to the other Janthinobacterium spp. Putatively identified horizontal gene transfer events contributed 0.92 Mb to the genome size expansion of Janthinobacterium sp. CG23_2. Genes with high copy numbers in the species-specific accessory genome of Janthinobacterium sp. CG23_2 were associated with environmental sensing, locomotion, response and transcriptional regulation, stress response, and mobile elements—functional categories which also showed molecular adaptation to cold. Our data suggest that genome plasticity and the abundant complementary genes for sensing and responding to the extracellular environment supported the adaptation of Janthinobacterium sp. CG23_2 to this extreme environment.

scholarly journals Differentially regulated orthologs in sorghum and the subgenomes of maize

2017 ◽  
Author(s):  
Yang Zhang ◽  
Daniel W. Ngu ◽  
Daniel Carvalho ◽  
Zhikai Liang ◽  
Yumou Qiu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Time Course ◽  
Purifying Selection ◽  
Micrococcal Nuclease ◽  
Open Chromatin ◽  
Transcriptional Responses ◽  
Hypersensitive Sites ◽  
Species Comparisons ◽  
Species Specific

AbstractCross-species comparisons of transcriptional regulation have the potential to identify functionally constrained transcriptional regulation and genes for which a change in transcriptional regulation correlates with a change in phenotype. Conventional differential gene expression analysis and a different approach based on identifying differentially regulated orthologs (DROs) are compared using paired time course gene expression data from two species which respond similarly to cold – maize (Zea mays) and sorghum (Sorghum bicolor). Both approaches suggest that, for genes conserved at syntenic positions for millions of years, the majority of cold responsive transcriptional regulation is species specific, although initial transcriptional responses to cold appear to be more conserved between the two species than later responses. In maize, the promoters of genes with both species specific and conserved transcriptional responses to cold tend to contain more micrococcal nuclease hypersensitive sites in their promoters, a proxy for open chromatin. However, genes with conserved patterns of transcriptional regulation between the two species show lower ratios of nonsynonymous to synonymous substitutions consistent with this population of genes experiencing stronger purifying selection. We hypothesize that cold responsive transcriptional regulation is a fast evolving and largely neutral molecular phenotype for the majority of genes in Andropogoneae, while a smaller core set of genes involved in perceiving and responding to cold stress are subject to functionally constrained cold responsive regulation.

scholarly journals Metagenomic Shotgun Analyses Reveal Complex Patterns of Intra- and Interspecific Variation in the Intestinal Microbiomes of Codfishes

2020 ◽  
Vol 86 (6) ◽  
Author(s):  
Even Sannes Riiser ◽  
Thomas H. A. Haverkamp ◽  
Srinidhi Varadharajan ◽  
Ørnulf Borgan ◽  
Kjetill S. Jakobsen ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Interspecific Variation ◽  
Shotgun Sequencing ◽  
Intestinal Microbiome ◽  
Ecological Niches ◽  
Content Type ◽  
Evolutionary Trajectories ◽  
Species Specific

ABSTRACT The relative importance of host-specific selection or environmental factors in determining the composition of the intestinal microbiome in wild vertebrates remains poorly understood. Here, we used metagenomic shotgun sequencing of individual specimens to compare the levels of intra- and interspecific variation of intestinal microbiome communities in two ecotypes (NEAC and NCC) of Atlantic cod (Gadus morhua) that have distinct behavior and habitats and three Gadidae species that occupy a range of ecological niches. Interestingly, we found significantly diverged microbiomes among the two Atlantic cod ecotypes. Interspecific patterns of variation are more variable, with significantly diverged communities for most species’ comparisons, apart from the comparison between coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose community compositions are not significantly diverged. The absence of consistent species-specific microbiomes suggests that external environmental factors, such as temperature, diet, or a combination thereof, comprise major drivers of the intestinal community composition of codfishes. IMPORTANCE The composition of the intestinal microbial community associated with teleost fish is influenced by a diversity of factors, ranging from internal factors (such as host-specific selection) to external factors (such as niche occupation). These factors are often difficult to separate, as differences in niche occupation (e.g., diet, temperature, or salinity) may correlate with distinct evolutionary trajectories. Here, we investigate four gadoid species with contrasting levels of evolutionary separation and niche occupation. Using metagenomic shotgun sequencing, we observed distinct microbiomes among two Atlantic cod (Gadus morhua) ecotypes (NEAC and NCC) with distinct behavior and habitats. In contrast, interspecific patterns of variation were more variable. For instance, we did not observe interspecific differentiation between the microbiomes of coastal cod (NCC) and Norway pout (Trisopterus esmarkii), whose lineages underwent evolutionary separation over 20 million years ago. The observed pattern of microbiome variation in these gadoid species is therefore most parsimoniously explained by differences in niche occupation.

scholarly journals Principles for enhancing virus capsid capacity and stability from a thermophilic virus capsid structure

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Nicholas P. Stone ◽  
Gabriel Demo ◽  
Emily Agnello ◽  
Brian A. Kelch
Keyword(s):  
Major Capsid Protein ◽  
Extreme Environment ◽  
Structural Basis ◽  
Genome Packaging ◽  
Virus Capsid ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
High Internal Pressure ◽  
Extracellular Environment ◽  
Catch Bonds

Abstract The capsids of double-stranded DNA viruses protect the viral genome from the harsh extracellular environment, while maintaining stability against the high internal pressure of packaged DNA. To elucidate how capsids maintain stability in an extreme environment, we use cryoelectron microscopy to determine the capsid structure of thermostable phage P74-26 to 2.8-Å resolution. We find P74-26 capsids exhibit an overall architecture very similar to those of other tailed bacteriophages, allowing us to directly compare structures to derive the structural basis for enhanced stability. Our structure reveals lasso-like interactions that appear to function like catch bonds. This architecture allows the capsid to expand during genome packaging, yet maintain structural stability. The P74-26 capsid has T = 7 geometry despite being twice as large as mesophilic homologs. Capsid capacity is increased with a larger, flatter major capsid protein. Given these results, we predict decreased icosahedral complexity (i.e. T ≤ 7) leads to a more stable capsid assembly.

scholarly journals Species-Specific Coral Calcification Responses to the Extreme Environment of the Southern Persian Gulf

2018 ◽  
Vol 5 ◽  
Author(s):  
Emily J. Howells ◽  
Glenn Dunshea ◽  
Dain McParland ◽  
Grace O. Vaughan ◽  
Scott F. Heron ◽  
...  
Keyword(s):  
Persian Gulf ◽  
Extreme Environment ◽  
Coral Calcification ◽  
Species Specific

scholarly journals Transcriptional Regulation of Divergent Capsule Biosynthesis and Transport Operon Promoters in Serogroup BNeisseria meningitidis

2001 ◽  
Vol 69 (4) ◽  
pp. 2502-2511 ◽  
Author(s):  
Yih-Ling Tzeng ◽  
John S. Swartley ◽  
Yoon K. Miller ◽  
Rachel E. Nisbet ◽  
Li-Jun Liu ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Sialic Acid ◽  
Stationary Phase ◽  
Intergenic Region ◽  
Direct Repeat ◽  
Intergenic Sequence ◽  
Transcriptional Level ◽  
Phase Growth ◽  
Specific Regulation ◽  
Species Specific

ABSTRACT The clinically important serogroups B, C, Y, and W-135 ofNeisseria meningitidis produce sialic acid capsules that are critical in pathogenesis. In each of these serogroups, the capsule transport (ctrABCD) and capsule biosynthesis (synABCD) operons are divergently transcribed from putative promoters located in a 134-bp intergenic region (J. S. Swartley, J. H. Ahn, L. J. Liu, C. M. Kahler, and D. S. Stephens, J. Bacteriol. 178:4052–4059, 1996). In this study we further assessed the role of the intergenic sequence in the transcriptional regulation of the sialic acid capsules of N. meningitidis. Insertional mutagenesis or deletions of the 134-bp sequence in the serogroup B meningococcal strain NMB resulted in a marked reduction or elimination of ctrABCD and synABCDtranscription, with a concomitant loss of encapsulation. Chromosomal transcriptional lacZ-ermC reporter fusions ofsyn and ctr promoters were constructed through allelic exchange. Using these constructs, both operons were found to be constitutively transcribed in meningococci, the biosynthesis operon about fourfold higher than the transport operon. Both promoters showed increased activity during stationary-phase growth. In addition to the promoters, a 70-bp 5′ untranslated region (UTR) upstream ofsynA was found to have a direct repeat and an inverted repeat that overlapped three putative integration host factor binding sites. Mutation of this 70-bp UTR and of the direct repeat upregulated both syn and ctr transcription. Regulation through the synA UTR was absent in a K1 Escherichia coli strain that produces identical capsular polysaccharide, implicating species-specific regulation. Meningococcal sialic acid capsule expression is initiated by divergent promoters in a 134-bp intergenic region, is repressed at the transcriptional level by the 5′ UTR of synA, is increased during stationary-phase growth, and shows species-specific regulation. Transcriptional regulation is another important control point for sialic capsule expression inN. meningitidis.

Anatomy of the endolithic Sonoran Desert lichen Verrucaria rubrocincta Breuss: implications for biodeterioration and biomineralization

2004 ◽  
Vol 36 (1) ◽  
pp. 55-73 ◽  
Author(s):  
Frank BUNGARTZ ◽  
Laurence A. J. GARVIE ◽  
Thomas H. NASH
Keyword(s):  
Sonoran Desert ◽  
Extreme Environment ◽  
Sensu Stricto ◽  
Combined Effects ◽  
Fine Grained ◽  
Calcium Oxalates ◽  
Environmental Extremes ◽  
Mineralogical Evidence ◽  
Thallus Surface ◽  
Scanning Electron

The anatomy of the endolithic, calcicolous lichen Verrucaria rubrocincta Breuss is described using optical and scanning electron microscopy. This lichen is locally abundant in caliche plates of open desert pavements in the Sonoran Desert of south-western Arizona. The endolithic growth of V. rubrocincta is distinctly layered. The upper layer is a fine-grained calcite (micrite). This layer is sparsely penetrated by hyphae and therefore cannot be interpreted as a lithocortex sensu stricto. Beneath the micrite is the photobiont layer. Below this photobiont layer hyphae form a pseudomedulla penetrating up to 1 cm into the caliche. Calcium oxalates occur in the pseudomedulla but are absent from uninhabited caliche. The analogy of a greenhouse describes the ecophysiological adaptations of this endolithic growth to the environmental extremes of the Sonoran Desert. The micrite acts as a roof and the photobiont layer and pseudomedulla represent the greenhouse interior. Verrucaria rubrocincta has thus evolved a strategy to successfully establish and survive within an extreme environment. Our study illustrates biodeterioration and biomineralization processes acting simultaneously within a single lichen species. Mineralogical evidence suggests that the micrite on the thallus surface is biologically induced. The hyphae of the lichen biodeteriorate the caliche thus forming the pseudomedulla. Simultaneously with this process micrite forms at the surface protecting the thallus from exposure and counter-balancing rock degradation. These combined effects of biodeterioration and biomineralization do not markedly accelerate erosion because inhabited and uninhabited areas of the same plate show similar surface heights.

scholarly journals Developmental expression of the 412 retrotransposon in natural populations of D. melanogaster and D. simulans

2000 ◽  
Vol 76 (3) ◽  
pp. 217-226 ◽  
Author(s):  
N. BORIE ◽  
C. LOEVENBRUCK ◽  
C. BIEMONT
Keyword(s):  
Expression Pattern ◽  
Copy Number ◽  
Developmental Stages ◽  
Population Sample ◽  
Natural Populations ◽  
Developmental Expression ◽  
Regulatory Sequences ◽  
Copy Numbers ◽  
Species Specific ◽  
Very High

We analysed the pattern of expression of retrotransposon 412 through developmental stages in various populations of Drosophila simulans and D. melanogaster differing in 412 copy number. We found that the 412 expression pattern varied greatly between populations of both species, indicating that such patterns were not entirely species-specific. In D. simulans, total transcripts increased with number of 412 copies in the chromosomes when this number was low, and then decreased for high copy numbers. D. melanogaster, which has a higher 412 copy number than D. simulans, had overall a lower global 412 expression, but again showed variation in 412 expression pattern between populations. These results suggest that in populations of D. simulans with low 412 copy number, the expression pattern of this element depends not only on copy number but also on host cellular regulatory sequences near which the elements were inserted. In D. simulans populations with high copy number overall transcription was on the contrary globally repressed, as observed in D. melanogaster. A population from Canberra (Australia) which had a very high 412 copy number was found to be associated with very high expression of 412 over all developmental stages, suggesting that the above 412 expression regulation processes are overcome in this population sample. The analysis of hybrids between geographically distinct populations of D. simulans showed that 412 expression was trans-regulated differently according to developmental stages, implying complex interactions between the 412 element and stage-specific host genes.

scholarly journals Comparative Genome Sequence Analysis Reveals the Extent of Diversity and Conservation for Glycan-Associated Proteins inBurkholderiaspp.

2012 ◽  
Vol 2012 ◽  
pp. 1-15 ◽  
Author(s):  
Hui San Ong ◽  
Rahmah Mohamed ◽  
Mohd Firdaus-Raih
Keyword(s):  
Comparative Analysis ◽  
Genome Sequence ◽  
Defense Mechanisms ◽  
Surface Proteins ◽  
Ecological Niches ◽  
Specific Gene ◽  
Sequence Comparisons ◽  
Virulence Protein ◽  
Associated Proteins ◽  
Species Specific

Members of theBurkholderiafamily occupy diverse ecological niches. In pathogenic family members, glycan-associated proteins are often linked to functions that include virulence, protein conformation maintenance, surface recognition, cell adhesion, and immune system evasion. Comparative analysis of availableBurkholderiagenomes has revealed a core set of 178 glycan-associated proteins shared by allBurkholderiaof which 68 are homologous to known essential genes. The genome sequence comparisons revealed insights into species-specific gene acquisitions through gene transfers, identified an S-layer protein, and proposed that significantly reactive surface proteins are associated to sugar moieties as a potential means to circumvent host defense mechanisms. The comparative analysis using a curated database of search queries enabled us to gain insights into the extent of conservation and diversity, as well as the possible virulence-associated roles of glycan-associated proteins in members of theBurkholderiaspp. The curated list of glycan-associated proteins used can also be directed to screen other genomes for glycan-associated homologs.

Cis-regulatory elements involved in species-specific transcriptional regulation of the SVCT1 gene in rat and human hepatoma cells

2015 ◽  
Vol 85 ◽  
pp. 183-196 ◽  
Author(s):  
Alejandra Muñoz ◽  
Marcelo Villagrán ◽  
Paula Guzmán ◽  
Carlos Solíz ◽  
Marcell Gatica ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Regulatory Elements ◽  
Hepatoma Cells ◽  
Human Hepatoma ◽  
Human Hepatoma Cells ◽  
Species Specific

scholarly journals A unified nomenclature for vertebrate olfactory receptors

2020 ◽  
Author(s):  
Tsviya Olender ◽  
Tamsin E.M. Jones ◽  
Elspeth Bruford ◽  
Doron Lancet
Keyword(s):  
Receptor Gene ◽  
Olfactory Receptors ◽  
Large Deletion ◽  
Ecological Niches ◽  
Gene Nomenclature ◽  
Nomenclature System ◽  
Or Gene ◽  
Species Specific ◽  
Or Genes ◽  
Genomic Cluster

Abstract Background Olfactory receptors (ORs) are G protein-coupled receptors with a crucial role in odor detection. A typical mammalian genome harbors ~1000 OR genes and pseudogenes; however, different gene duplication/deletion events have occurred in each species, resulting in complex orthology relationships. While the human OR nomenclature is widely accepted and based on phylogenetic classification into 18 families and further into subfamilies, for other mammals different and multiple nomenclature systems are currently in use, thus concealing important evolutionary and functional insights. Results Here we describe the Mutual Maximum Similarity (MMS) algorithm, a systematic classifier for assigning a human-centric nomenclature to any OR gene based on inter-species hierarchical pairwise similarities. MMS was applied to the OR repertoires of seven mammals and zebrafish. Altogether, we assigned symbols to 10,249 ORs. This nomenclature is supported by both phylogenetic and synteny analyses. The availability of a unified nomenclature provides a framework for diverse studies, where textual symbol comparison allows immediate identification of potential ortholog groups as well as species-specific expansions/deletions; for example, Or52e5 and Or52e5b represent a rat-specific duplication of OR52E5 . Another example is the complete absence of OR subfamily OR6Z among primate OR symbols. In other mammals, OR6Z members are located in one genomic cluster, suggesting a large deletion in the great ape lineage. An additional 14 mammalian OR subfamilies are missing from the primate genomes. While in chimpanzee 87% of the symbols were identical to human symbols, this number decreased to ~50% in dog and cow and to ~30% in rodents, reflecting the adaptive changes of the OR gene superfamily across diverse ecological niches. Application of the proposed nomenclature to zebrafish revealed similarity to mammalian ORs that could not be detected from the current zebrafish olfactory receptor gene nomenclature. Conclusions We have consolidated a unified standard nomenclature system for the vertebrate OR superfamily. The new nomenclature system will be applied to cow, horse, dog and chimpanzee by the Vertebrate Gene Nomenclature Committee and its implementation is currently under consideration by other relevant species-specific nomenclature committees.

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