scholarly journals Natural strain variation reveals diverse biofilm regulation in squid-colonizingVibrio fischeri

2018 ◽  
Author(s):  
Ella R. Rotman ◽  
Katherine M. Bultman ◽  
John F. Brooks ◽  
Mattias C. Gyllborg ◽  
Hector L. Burgos ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Antimicrobial Agents ◽  
Vibrio Fischeri ◽  
Dynamic Regulation ◽  
Evolutionary Transitions ◽  
Regulatory Changes ◽  
Natural Isolates ◽  
Group A ◽  
Bacterial Aggregates ◽  
Hybrid Histidine Kinase

ABSTRACTThe mutualistic symbiontVibrio fischeribuilds a symbiotic biofilm during colonization of squid hosts. Regulation of the exopolysaccharide component, termed Syp, has been examined in strain ES114, where production is controlled by a phosphorelay that includes the inner membrane hybrid histidine kinase RscS. Most strains that lack RscS or encode divergent RscS proteins cannot colonize a squid host unless RscS from a squid symbiont is heterologously expressed. In this study, we examineV. fischeriisolates worldwide to understand the landscape of biofilm regulation during beneficial colonization. We provide a detailed study of three distinct evolutionary groups ofV. fischeriand find that while the RscS-Syp biofilm pathway is required in one of the groups, two other groups of squid symbionts require Syp independent of RscS. Mediterranean squid symbionts, includingV. fischeriSR5, colonize without an RscS homolog encoded in their genome. Additionally, Group AV. fischeristrains, which form a tightly-related clade of Hawaii isolates, have a frameshift inrscSand do not require the gene for squid colonization or competitive fitness. These same strains have a frameshift insypE, and we provide evidence that this Group AsypEallele leads to an upregulation in biofilm activity. This work thus describes the central importance of Syp biofilm in colonization of diverse isolates, and demonstrates that significant evolutionary transitions correspond to regulatory changes in thesyppathway.IMPORTANCEBiofilms are surface-associated, matrix-encased bacterial aggregates that exhibit enhanced protection to antimicrobial agents. Previous work has established the importance of biofilm formation by a strain of luminousVibrio fischeribacteria as the bacteria colonize their host, the Hawaiian bobtail squid. In this study, expansion of this work to many natural isolates revealed that biofilm genes are universally required, yet there has been a shuffling of the regulators of those genes. This work provides evidence that even when bacterial behaviors are conserved, dynamic regulation of those behaviors can underlie evolution of the host colonization phenotype. Furthermore, this work emphasizes the importance of investigating natural diversity as we seek to understand molecular mechanisms in bacteria.

scholarly journals Natural Strain Variation Reveals Diverse Biofilm Regulation in Squid-ColonizingVibrio fischeri

2019 ◽  
Vol 201 (9) ◽  
Author(s):  
Ella R. Rotman ◽  
Katherine M. Bultman ◽  
John F. Brooks ◽  
Mattias C. Gyllborg ◽  
Hector L. Burgos ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Antimicrobial Agents ◽  
Vibrio Fischeri ◽  
Dynamic Regulation ◽  
Evolutionary Transitions ◽  
Content Type ◽  
Regulatory Changes ◽  
Natural Isolates ◽  
Group A ◽  
Bacterial Aggregates

ABSTRACTThe mutualistic symbiontVibrio fischeribuilds a symbiotic biofilm during colonization of squid hosts. Regulation of the exopolysaccharide component, termed Syp, has been examined in strain ES114, where production is controlled by a phosphorelay that includes the inner membrane hybrid histidine kinase RscS. Most strains that lack RscS or encode divergent RscS proteins cannot colonize a squid host unless RscS from a squid symbiont is heterologously expressed. In this study, we examineV. fischeriisolates worldwide to understand the landscape of biofilm regulation during beneficial colonization. We provide a detailed study of three distinct evolutionary groups ofV. fischeriand find that while the RscS-Syp biofilm pathway is required in one of the groups, two other groups of squid symbionts require Syp independent of RscS. Mediterranean squid symbionts, includingV. fischeriSR5, colonize without an RscS homolog encoded by their genome. Additionally, group AV. fischeristrains, which form a tightly related clade of Hawaii isolates, have a frameshift inrscSand do not require the gene for squid colonization or competitive fitness. These same strains have a frameshift insypE, and we provide evidence that this group AsypEallele leads to an upregulation in biofilm activity. Thus, this work describes the central importance of Syp biofilm in colonization of diverse isolates and demonstrates that significant evolutionary transitions correspond to regulatory changes in thesyppathway.IMPORTANCEBiofilms are surface-associated, matrix-encased bacterial aggregates that exhibit enhanced protection to antimicrobial agents. Previous work has established the importance of biofilm formation by a strain of luminousVibrio fischeribacteria as the bacteria colonize their host, the Hawaiian bobtail squid. In this study, expansion of this work to many natural isolates revealed that biofilm genes are universally required, yet there has been a shuffling of the regulators of those genes. This work provides evidence that even when bacterial behaviors are conserved, dynamic regulation of those behaviors can underlie evolution of the host colonization phenotype. Furthermore, this work emphasizes the importance of investigating natural diversity as we seek to understand molecular mechanisms in bacteria.

scholarly journals Multidrug Antimicrobial Resistance and Molecular Detection of mcr-1 Gene in Salmonella Species Isolated from Chicken

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 206
Author(s):  
Md Bashir Uddin ◽  
S.M. Bayejed Hossain ◽  
Mahmudul Hasan ◽  
Mohammad Nurul Alam ◽  
Mita Debnath ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Antimicrobial Resistance ◽  
In Silico ◽  
Salmonella Enterica ◽  
Molecular Mechanisms ◽  
Antimicrobial Agents ◽  
Genetic Relationships ◽  
Evolutionary Relationship ◽  
Salmonella Spp ◽  
Gram Negative

Colistin (polymyxin E) is widely used in animal and human medicine and is increasingly used as one of the last-resort antibiotics against Gram-negative bacilli. Due to the increased use of colistin in treating infections caused by multidrug-resistant Gram-negative bacteria, resistance to this antibiotic ought to be monitored. The study was undertaken to elucidate the molecular mechanisms, genetic relationships and phenotype correlations of colistin-resistant isolates. Here, we report the detection of the mcr-1 gene in chicken-associated Salmonella isolates in Bangladesh and its in-silico functional analysis. Out of 100 samples, 82 Salmonella spp. were isolated from chicken specimens (liver, intestine). Phenotypic disc diffusion and minimum inhibitory concentration (MIC) assay using different antimicrobial agents were performed. Salmonella isolates were characterized using PCR methods targeting genus-specific invA and mcr-1 genes with validation for the functional analysis. The majority of the tested Salmonella isolates were found resistant to colistin (92.68%), ciprofloxacin (73.17%), tigecycline (62.20%) and trimethoprim/sulfamethoxazole (60.98%). When screened using PCR, five out of ten Salmonella isolates were found to carry the mcr-1 gene. One isolate was confirmed for Salmonella enterica subsp. enterica serovar Enteritidis, and other four isolates were confirmed for Salmonella enterica subsp. enterica serovar Typhimurium. Sequencing and phylogenetic analysis revealed a divergent evolutionary relationship between the catalytic domain of Neisseria meningitidis lipooligosaccharide phosphoethanolamine transferase A (LptA) and MCR proteins, rendering them resistant to colistin. Three-dimensional homology structural analysis of MCR-1 proteins and molecular docking interactions suggested that MCR-1 and LptA share a similar substrate binding cavity, which could be validated for the functional analysis. The comprehensive molecular and in-silico analyses of the colistin resistance mcr-1 gene of Salmonella spp. of chicken origin in the present study highlight the importance of continued monitoring and surveillance for antimicrobial resistance among pathogens in food chain animals.

scholarly journals Natural Disruption of Two Regulatory Networks in Serotype M3 Group A Streptococcus Isolates Contributes to the Virulence Factor Profile of This Hypervirulent Serotype

2014 ◽  
Vol 82 (5) ◽  
pp. 1744-1754 ◽  
Author(s):  
Tram N. Cao ◽  
Zhuyun Liu ◽  
Tran H. Cao ◽  
Kathryn J. Pflughoeft ◽  
Jeanette Treviño ◽  
...  
Keyword(s):  
Virulence Factor ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Group A Streptococcus ◽  
Regulatory System ◽  
Mrna Levels ◽  
Bacterial Strains ◽  
Content Type ◽  
Small Regulatory Rna ◽  
Group A

ABSTRACTDespite the public health challenges associated with the emergence of new pathogenic bacterial strains and/or serotypes, there is a dearth of information regarding the molecular mechanisms that drive this variation. Here, we began to address the mechanisms behind serotype-specific variation between serotype M1 and M3 strains of the human pathogenStreptococcus pyogenes(the group AStreptococcus[GAS]). Spatially diverse contemporary clinical serotype M3 isolates were discovered to contain identical inactivating mutations within genes encoding two regulatory systems that control the expression of important virulence factors, including the thrombolytic agent streptokinase, the protease inhibitor-binding protein-G-related α2-macroglobulin-binding (GRAB) protein, and the antiphagocytic hyaluronic acid capsule. Subsequent analysis of a larger collection of isolates determined that M3 GAS, since at least the 1920s, has harbored a 4-bp deletion in thefasCgene of thefasBCAXregulatory system and an inactivating polymorphism in therivRregulator-encoding gene. ThefasCandrivRmutations in M3 isolates directly affect the virulence factor profile of M3 GAS, as evident by a reduction in streptokinase expression and an enhancement of GRAB expression. Complementation of thefasCmutation in M3 GAS significantly enhanced levels of the small regulatory RNA FasX, which in turn enhanced streptokinase expression. Complementation of therivRmutation in M3 GAS restored the regulation ofgrabmRNA abundance but did not alter capsule mRNA levels. While important, thefasCandrivRmutations do not provide a full explanation for why serotype M3 strains are associated with unusually severe invasive infections; thus, further investigation is warranted.

Evolution of stickleback spines through independent cis-regulatory changes at HOXDB

2021 ◽  
Author(s):  
Julia I Wucherpfennig ◽  
Timothy R Howes ◽  
Jessica N Au ◽  
Eric H Au ◽  
Garrett A Roberts Kingman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Evolutionary Biology ◽  
Gasterosteus Aculeatus ◽  
Molecular Mechanisms ◽  
Wild Populations ◽  
Gene Variation ◽  
Regulatory Changes ◽  
Fundamental Goal ◽  
Apeltes Quadracus ◽  
Genetic Mechanisms

Understanding the genetic mechanisms leading to new traits is a fundamental goal of evolutionary biology. We show that HOXDB regulatory changes have been used repeatedly in different stickleback fish species to alter the length and number of bony dorsal spines. In Gasterosteus aculeatus, a variant HOXDB allele is genetically linked to shortening an existing spine and adding a spine. In Apeltes quadracus, a variant allele is associated with lengthening an existing spine and adding a spine. The alleles alter the same conserved non-coding HOXDB enhancer by diverse molecular mechanisms, including SNPs, deletions, and transposable element insertions. The independent cis-acting regulatory changes are linked to anterior expansion or contraction of HOXDB expression. Our findings support the long-standing hypothesis that natural Hox gene variation underlies key morphological patterning changes in wild populations and illustrate how different mutational mechanisms affecting the same region may produce opposite gene expression changes with similar phenotypic outcomes.

scholarly journals Bacterial symbionts use a type VI secretion system to eliminate competitors in their natural host

2018 ◽  
Vol 115 (36) ◽  
pp. E8528-E8537 ◽  
Author(s):  
Lauren Speare ◽  
Andrew G. Cecere ◽  
Kirsten R. Guckes ◽  
Stephanie Smith ◽  
Michael S. Wollenberg ◽  
...  
Keyword(s):  
Intraspecific Competition ◽  
Vibrio Fischeri ◽  
Secretion System ◽  
Dependent Manner ◽  
Light Organ ◽  
Type Vi Secretion System ◽  
Type Vi Secretion ◽  
Natural Isolates ◽  
Physical Mixing

Intraspecific competition describes the negative interaction that occurs when different populations of the same species attempt to fill the same niche. Such competition is predicted to occur among host-associated bacteria but has been challenging to study in natural biological systems. Although many bioluminescentVibrio fischeristrains exist in seawater, only a few strains are found in the light-organ crypts of an individual wild-caughtEuprymna scolopessquid, suggesting a possible role for intraspecific competition during early colonization. Using a culture-based assay to investigate the interactions of differentV. fischeristrains, we found “lethal” and “nonlethal” isolates that could kill or not kill the well-studied light-organ isolate ES114, respectively. The killing phenotype of these lethal strains required a type VI secretion system (T6SS) encoded in a 50-kb genomic island. Multiple lethal and nonlethal strains could be cultured from the light organs of individual wild-caught adult squid. Although lethal strains eliminate nonlethal strains in vitro, two lethal strains could coexist in interspersed microcolonies that formed in a T6SS-dependent manner. This coexistence was destabilized upon physical mixing, resulting in one lethal strain consistently eliminating the other. When juvenile squid were coinoculated with lethal and nonlethal strains, they occupied different crypts, yet they were observed to coexist within crypts when T6SS function was disrupted. These findings, using a combination of natural isolates and experimental approaches in vitro and in the animal host, reveal the importance of T6SS in spatially separating strains during the establishment of host colonization in a natural symbiosis.

scholarly journals Molecular mechanisms for microtubule length regulation by kinesin-8 and XMAP215 proteins

2014 ◽  
Vol 4 (6) ◽  
pp. 20140031 ◽  
Author(s):  
Louis Reese ◽  
Anna Melbinger ◽  
Erwin Frey
Keyword(s):  
Molecular Motors ◽  
Molecular Mechanisms ◽  
Molecular Motor ◽  
Mutual Exclusion ◽  
High Growth ◽  
Dependent Manner ◽  
Dynamic Regulation ◽  
Filament Dynamics ◽  
Length Regulation ◽  
The Stability

The cytoskeleton is regulated by a plethora of enzymes that influence the stability and dynamics of cytoskeletal filaments. How microtubules (MTs) are controlled is of particular importance for mitosis, during which dynamic MTs are responsible for proper segregation of chromosomes. Molecular motors of the kinesin-8 protein family have been shown to depolymerize MTs in a length-dependent manner, and recent experimental and theoretical evidence suggests a possible role for kinesin-8 in the dynamic regulation of MTs. However, so far the detailed molecular mechanisms of how these molecular motors interact with the growing MT tip remain elusive. Here we show that two distinct scenarios for the interactions of kinesin-8 with the MT tip lead to qualitatively different MT dynamics, including accurate length control as well as intermittent dynamics. We give a comprehensive analysis of the regimes where length regulation is possible and characterize how the stationary length depends on the biochemical rates and the bulk concentrations of the various proteins. For a neutral scenario, where MTs grow irrespective of whether the MT tip is occupied by a molecular motor, length regulation is possible only for a narrow range of biochemical rates, and, in particular, limited to small polymerization rates. By contrast, for an inhibition scenario, where the presence of a motor at the MT tip inhibits MT growth, the regime where length regulation is possible is extremely broad and includes high growth rates. These results also apply to situations where a polymerizing enzyme like XMAP215 and kinesin-8 mutually exclude each other from the MT tip. Moreover, we characterize the differences in the stochastic length dynamics between the two scenarios. While for the neutral scenario length is tightly controlled, length dynamics is intermittent for the inhibition scenario and exhibits extended periods of MT growth and shrinkage. On a broader perspective, the set of models established in this work quite generally suggest that mutual exclusion of molecules at the ends of cytoskeletal filaments is an important factor for filament dynamics and regulation.

scholarly journals Tissue-specific cis-regulatory divergence implicates a fatty acid elongase necessary for inhibiting interspecies mating in Drosophila

2018 ◽  
Author(s):  
Peter A. Combs ◽  
Joshua J. Krupp ◽  
Neil M. Khosla ◽  
Dennis Bua ◽  
Dmitri A. Petrov ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Sister Species ◽  
F1 Hybrids ◽  
Rna Seq ◽  
Fatty Acid Elongase ◽  
Tissue Specific ◽  
Regulatory Changes ◽  
Wide Range

AbstractPheromones known as cuticular hydrocarbons are a major component of reproductive isolation in Drosophila. Individuals from morphologically similar sister species produce different sets of hydrocarbons that allow potential mates to identify them as a suitable partner. In order to explore the molecular mechanisms underlying speciation, we performed RNA-seq in F1 hybrids to measure tissue-specific cis-regulatory divergence between the sister species D. simulans and D. sechellia. By focusing on cis-regulatory changes specific to female oenocytes, we rapidly identified a small number of candidate genes. We found that one of these, the fatty acid elongase eloF, broadly affects both the complement of hydrocarbons present on D. sechellia females and the propensity of D. simulans males to mate with those females. In addition, knockdown of eloF in the more distantly related D. melanogaster led to a similar shift in hydrocarbons as well as lower interspecific mate discrimination by D. simulans males. Thus, cis-regulatory changes in eloF appear to be a major driver in the sexual isolation of D. simulans from multiple other species. More generally, our RNA-seq approach proved to be far more efficient than QTL mapping in identifying candidate genes; the same framework can be used to pinpoint cis-regulatory drivers of divergence in a wide range of traits differing between any interfertile species.

scholarly journals Transcriptomic Modification in the Cerebral Cortex following Noninvasive Brain Stimulation: RNA-Sequencing Approach

2016 ◽  
Vol 2016 ◽  
pp. 1-15 ◽  
Author(s):  
Ben Holmes ◽  
Seung Ho Jung ◽  
Jing Lu ◽  
Jessica A. Wagner ◽  
Liudmilla Rubbi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cerebral Cortex ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Current Intensity ◽  
Beneficial Effects ◽  
Group A ◽  
The Impact

Transcranial direct current stimulation (tDCS) has been shown to modulate neuroplasticity. Beneficial effects are observed in patients with psychiatric disorders and enhancement of brain performance in healthy individuals has been observed following tDCS. However, few studies have attempted to elucidate the underlying molecular mechanisms of tDCS in the brain. This study was conducted to assess the impact of tDCS on gene expression within the rat cerebral cortex. Anodal tDCS was applied at 3 different intensities followed by RNA-sequencing and analysis. In each current intensity, approximately 1,000 genes demonstrated statistically significant differences compared to the sham group. A variety of functional pathways, biological processes, and molecular categories were found to be modified by tDCS. The impact of tDCS on gene expression was dependent on current intensity. Results show that inflammatory pathways, antidepressant-related pathways (GTP signaling, calcium ion binding, and transmembrane/signal peptide pathways), and receptor signaling pathways (serotonergic, adrenergic, GABAergic, dopaminergic, and glutamate) were most affected. Of the gene expression profiles induced by tDCS, some changes were observed across multiple current intensities while other changes were unique to a single stimulation intensity. This study demonstrates that tDCS can modify the expression profile of various genes in the cerebral cortex and that these tDCS-induced alterations are dependent on the current intensity applied.

Redescription of The Southern Dumpling SquidEuprymna Tasmanicaand A Revision of The GenusEuprymna(Cephalopoda: Sepiolidae)

1997 ◽  
Vol 77 (4) ◽  
pp. 1109-1137 ◽  
Author(s):  
M.D. Norman ◽  
C.C. Lu
Keyword(s):  
Vibrio Fischeri ◽  
Taxonomic Status ◽  
Valid Species ◽  
Nominal Species ◽  
Undescribed Species ◽  
Additional Species ◽  
Symbiotic Associations ◽  
Luminescent Bacteria ◽  
Group A ◽  
Recent Attention

Recent attention to members of the sepiolid squid genusEuprymnaand symbiotic associations with luminescent bacteria (Vibrio fischeristrains) has prompted a review of this poorly-resolved group of squids. Twelve nominal species have been placed in this genus of which the majority are ill-defined, known only from their original descriptions and separated on the basis of inadequate characters. As a first step in resolving this group, a temperate Australian species, the Southern dumpling squid,Euprymna tasmanica, is here redescribed in detail. As the genusEuprymnacurrently stands, most members are only distinguished on the number and position of enlarged suckers in mature males. No diagnostic characters are available to identify females. All nominal species placed in this genus are reviewed and a key to proposed valid species is presented. Six species are considered here to be valid:Euprymna berryi, E. hoylei, E. morsei, E. scolopes, E. tasmanicaand an undescribed species treated here asEuprymnasp. 1.Euprymna similisis a synonym ofE. morseiof Japan. Due to inadequate original descriptions, and lost or poor type material, two species are considered here to benomen dubia(E. schneehageniandE. pusilla), while the taxonomic status of four additional species remain unresolved (E. albatrossae, E. bursa, E. phenaxandE. stenodactyla).

scholarly journals Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides

2018 ◽  
Author(s):  
Marta Kulik ◽  
Takaharu Mori ◽  
Yuji Sugita ◽  
Joanna Trylska
Keyword(s):  
Molecular Mechanisms ◽  
Dynamic Regulation
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