scholarly journals A model Roseobacter employs a diffusible killing mechanism to eliminate competitors

2019 ◽  
Author(s):  
Garrett C. Sharpe ◽  
Scott M. Gifford ◽  
Alecia N. Septer
Keyword(s):  
Gene Cluster ◽  
Structure And Function ◽  
Marine Ecology ◽  
Roseobacter Clade ◽  
Antimicrobial Compound ◽  
Wild Type ◽  
Sensing Systems ◽  
Transposon Mutants ◽  
Ruegeria Pomeroyi ◽  
And Function

AbstractThe roseobacter clade is a group of α-proteobacteria that have diverse metabolic and regulatory capabilities. They are abundant in marine environments and have a substantial role in marine ecology and biogeochemistry. However, interactions between roseobacters and other bacterioplankton have not been extensively explored. In this study, we identify a killing mechanism in the model Roseobacter Ruegeria pomeroyi DSS-3 by competing it against a group of phylogenetically diverse bacteria. The killing mechanism involves an unidentified antimicrobial compound that is produced when cells are grown on both surfaces and in suspension and is dependent on cell density. A screen of random transposon mutants revealed the killing phenotype, as well as resistance to the antimicrobial, require genes within an ~8 kb putative γ-butyrolactone synthesis gene cluster, which resembles similar pheromone-sensing systems in actinomycetes that regulate secondary metabolite production. Transcriptomics revealed the gene cluster is highly upregulated in wild-type DSS-3 compared to a non-killer mutant when grown in liquid coculture with a roseobacter target. Our findings show that R. pomeroyi has the capability to eliminate closely- and distantly-related competitors, providing a mechanism to alter the community structure and function in its native habitats.

scholarly journals A Model Roseobacter, Ruegeria pomeroyi DSS-3, Employs a Diffusible Killing Mechanism To Eliminate Competitors

mSystems ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Garrett C. Sharpe ◽  
Scott M. Gifford ◽  
Alecia N. Septer
Keyword(s):  
Gene Cluster ◽  
Microbial Community Composition ◽  
Marine Ecology ◽  
Bacterial Populations ◽  
Content Type ◽  
Functional Capabilities ◽  
Regulatory Strategies ◽  
Transposon Mutants ◽  
Ruegeria Pomeroyi ◽  
And Function

ABSTRACT The Roseobacter clade is a group of alphaproteobacteria that have diverse metabolic and regulatory capabilities. They are abundant in marine environments and have a substantial role in marine ecology and biogeochemistry. However, interactions between roseobacters and other bacterioplankton have not been extensively explored. In this study, we identify a killing mechanism in the model roseobacter Ruegeria pomeroyi DSS-3 by coculturing it with a group of phylogenetically diverse bacteria. The killing mechanism is diffusible and occurs when cells are grown both on surfaces and in suspension and is dependent on cell density. A screen of random transposon mutants revealed that the killing phenotype, as well as resistance to killing, require genes within an ∼8-kb putative gamma-butyrolactone synthesis gene cluster, which resembles similar pheromone-sensing systems in actinomycetes that regulate secondary metabolite production, including antimicrobials. Transcriptomics revealed the gene cluster is highly upregulated in wild-type DSS-3 compared to a nonkiller mutant when grown in liquid coculture with a roseobacter target. Our findings show that R. pomeroyi has the capability to eliminate closely and distantly related competitors, providing a mechanism to alter the community structure and function in its native habitats. IMPORTANCE Bacteria carry out critical ecological and biogeochemical processes and form the foundations of ecosystems. Identifying the factors that influence microbial community composition and the functional capabilities encoded within them is key to predicting how microbes impact an ecosystem. Because microorganisms must compete for limited space and nutrients to promote their own propagation, they have evolved diverse mechanisms to outcompete or kill competitors. However, the genes and regulatory strategies that promote such competitive abilities are largely underexplored, particularly in free-living marine bacteria. Here, genetics and omics techniques are used to investigate how a model marine bacterium is capable of quickly eliminating natural competitors in coculture. We determined that a previously uncharacterized horizontally acquired gene cluster is required for this bacterium to kill diverse competitors. This work represents an important step toward understanding the mechanisms bacterial populations can use to become dominant members in marine microbial communities.

scholarly journals A Rubisco-binding protein is required for normal pyrenoid number and starch sheath morphology inChlamydomonas reinhardtii

2019 ◽  
Vol 116 (37) ◽  
pp. 18445-18454 ◽  
Author(s):  
Alan K. Itakura ◽  
Kher Xing Chan ◽  
Nicky Atkinson ◽  
Leif Pallesen ◽  
Lianyong Wang ◽  
...  
Keyword(s):  
Surface Area ◽  
Structure And Function ◽  
Binding Motif ◽  
Starch Granules ◽  
Wild Type ◽  
Bisphosphate Carboxylase ◽  
Biophysical Mechanism ◽  
Mechanism Function ◽  
And Function

A phase-separated, liquid-like organelle called the pyrenoid mediates CO2fixation in the chloroplasts of nearly all eukaryotic algae. While most algae have 1 pyrenoid per chloroplast, here we describe a mutant in the model algaChlamydomonasthat has on average 10 pyrenoids per chloroplast. Characterization of the mutant leads us to propose a model where multiple pyrenoids are favored by an increase in the surface area of the starch sheath that surrounds and binds to the liquid-like pyrenoid matrix. We find that the mutant’s phenotypes are due to disruption of a gene, which we call StArch Granules Abnormal 1 (SAGA1) because starch sheath granules, or plates, in mutants lacking SAGA1 are more elongated and thinner than those of wild type. SAGA1 contains a starch binding motif, suggesting that it may directly regulate starch sheath morphology. SAGA1 localizes to multiple puncta and streaks in the pyrenoid and physically interacts with the small and large subunits of the carbon-fixing enzyme Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase), a major component of the liquid-like pyrenoid matrix. Our findings suggest a biophysical mechanism by which starch sheath morphology affects pyrenoid number and CO2-concentrating mechanism function, advancing our understanding of the structure and function of this biogeochemically important organelle. More broadly, we propose that the number of phase-separated organelles can be regulated by imposing constraints on their surface area.

scholarly journals Alterations in flight muscle ultrastructure and function in Drosophila tropomyosin mutants.

1996 ◽  
Vol 135 (3) ◽  
pp. 673-687 ◽  
Author(s):  
A J Kreuz ◽  
A Simcox ◽  
D Maughan
Keyword(s):  
Amino Acid ◽  
Power Output ◽  
Flight Muscle ◽  
Structure And Function ◽  
Wild Type ◽  
Muscle Tropomyosin ◽  
Ultrastructure And Function ◽  
And Function ◽  
Net Power Output ◽  
Current Report

Drosophila indirect flight muscle (IFM) contains two different types of tropomyosin: a standard 284-amino acid muscle tropomyosin, Ifm-TmI, encoded by the TmI gene, and two > 400 amino acid tropomyosins, TnH-33 and TnH-34, encoded by TmII. The two IFM-specific TnH isoforms are unique tropomyosins with a COOH-terminal extension of approximately 200 residues which is hydrophobic and rich in prolines. Previous analysis of a hypomorphic TmI mutant, Ifm(3)3, demonstrated that Ifm-TmI is necessary for proper myofibrillar assembly, but no null TmI mutant or TmII mutant which affects the TnH isoforms have been reported. In the current report, we show that four flightless mutants (Warmke et al., 1989) are alleles of TmI, and characterize a deficiency which deletes both TmI and TmII. We find that haploidy of TmI causes myofibrillar disruptions and flightless behavior, but that haploidy of TmII causes neither. Single fiber mechanics demonstrates that power output is much lower in the TmI haploid line (32% of wild-type) than in the TmII haploid line (73% of wild-type). In myofibers nearly depleted of Ifm-TmI, net power output is virtually abolished (< 1% of wild-type) despite the presence of an organized fibrillar core (approximately 20% of wild-type). The results suggest Ifm-TmI (the standard tropomyosin) plays a key role in fiber structure, power production, and flight, with reduced Ifm-TmI expression producing corresponding changes of IFM structure and function. In contrast, reduced expression of the TnH isoforms has an unexpectedly mild effect on IFM structure and function.

scholarly journals The plant circadian clock influences rhizosphere community structure and function

2017 ◽  
Author(s):  
Charley J. Hubbard ◽  
Marcus T. Brock ◽  
Linda T.A. van Diepen ◽  
Loïs Maignien ◽  
Brent E. Ewers ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Circadian Clock ◽  
Structure And Function ◽  
Plant Performance ◽  
Wild Type ◽  
Night Time ◽  
History Of ◽  
And Function ◽  
Rhizosphere Community

AbstractPlants alter chemical and physical properties of soil, and thereby influence rhizosphere microbial community structure. The structure of microbial communities may in turn affect plant performance. Yet, outside of simple systems with pairwise interacting partners, the plant genetic pathways that influence microbial community structure remain largely unknown, as are the performance feedbacks of microbial communities selected by the host plant genotype. We investigated the role of the plant circadian clock in shaping rhizosphere community structure and function. We performed 16S rRNA gene sequencing to characterize rhizosphere bacterial communities of Arabidopsis thaliana between day and night time points, and tested for differences in community structure between wild-type (Ws) vs. clock mutant (toc1-21, ztl-30) genotypes. We then characterized microbial community function, by growing wild-type plants in soils with an overstory history of Ws, toc1-21 or ztl-30 and measuring plant performance. We observed that rhizosphere community structure varied between day and night time points, and clock misfunction significantly altered rhizosphere communities. Finally, wild-type plants germinated earlier and were larger when inoculated with soils having an overstory history of wild-type in comparison to clock mutant genotypes. Our findings suggest the circadian clock of the plant host influences rhizosphere community structure and function.

scholarly journals Muscles of mice deficient in α-sarcoglycan maintain large masses and near control force values throughout the life span

2005 ◽  
Vol 22 (2) ◽  
pp. 244-256 ◽  
Author(s):  
Christina M. Consolino ◽  
Franck Duclos ◽  
Jane Lee ◽  
Roger A. Williamson ◽  
Kevin P. Campbell ◽  
...  
Keyword(s):  
Connective Tissue ◽  
Life Span ◽  
Structure And Function ◽  
Null Mouse ◽  
Control Force ◽  
Wild Type ◽  
Cross Sectional ◽  
Muscle Structure ◽  
And Function

α-Sarcoglycan-deficient ( Sgca-null) mice provide potential for elucidating the pathogenesis of limb girdle muscular dystrophy type 2D (LGMD 2D) as well as for studying the effectiveness of therapeutic strategies. Skeletal muscles of Sgca-null mice demonstrate an early onset of extensive fiber necrosis, degeneration, and regeneration, but the progression of the pathology and the effects on muscle structure and function throughout the life span are not known. Thus the phenotypic accuracy of the Sgca-null mouse as a model of LGMD 2D has not been fully established. To investigate skeletal muscle structure and function in the absence of α-sarcoglycan throughout the life span, we analyzed extensor digitorum longus and soleus muscles of male and female Sgca-null and wild-type mice at 3, 6, 12, and 18 mo of age. Maximum isometric forces and powers were measured in vitro at 25°C. Also determined were individual myofiber cross-sectional areas and numbers, water content, and the proportion of the cross section occupied by connective tissue. Muscle masses were 40–100% larger for Sgca-null compared with age- and gender-matched wild-type mice, with the majority of the increased muscle mass for Sgca-null mice attributable to greater connective tissue and water contents. Although the greater mass of muscles in Sgca-null mice was primarily noncontractile material, absolute forces and powers were maintained near control levels at all ages, indicating a successful adaptation to the deficiency in α-sarcoglycan not observed at any age in LGMD 2D patients.

The Structure and Function of Murine Factor V and Its Inactivation by Protein C

Blood ◽  
1998 ◽  
Vol 91 (12) ◽  
pp. 4593-4599 ◽  
Author(s):  
Tony L. Yang ◽  
Jisong Cui ◽  
Alnawaz Rehumtulla ◽  
Angela Yang ◽  
Micheline Moussalli ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein C ◽  
Mammalian Species ◽  
Structure And Function ◽  
Procoagulant Activity ◽  
Factor V ◽  
Cleavage Sites ◽  
Wild Type ◽  
Coding Region ◽  
And Function

Factor V (FV) is a central regulator of hemostasis, serving both as a critical cofactor for the prothrombinase activity of factor Xa and the target for proteolytic inactivation by the anticoagulant, activated protein C (APC). To examine the evolutionary conservation of FV procoagulant activity and functional inactivation by APC, we cloned and sequenced the coding region of murine FV cDNA and generated recombinant wild-type and mutant murine FV proteins. The murine FV cDNA encodes a 2,183-amino acid protein. Sequence comparison shows that the A1-A3 and C1-C2 domains of FV are highly conserved, demonstrating greater than 84% sequence identity between murine and human, and 60% overall amino acid identity among human, bovine, and murine FV sequences. In contrast, only 35% identity among all three species is observed for the poorly conserved B domain. The arginines at all thrombin cleavage sites and the R305 and R504 APC cleavage sites (corresponding to amino acid residues R306 and R506 in human FV) are invariant in all three species. Point mutants were generated to substitute glutamine at R305, R504, or both (R305/R504). Wild-type and all three mutant FV recombinant proteins show equivalent FV procoagulant activity. Single mutations at R305 or R504 result in partial resistance of FV to APC inactivation, whereas recombinant murine FV carrying both mutations (R305Q/R504Q) is nearly completely APC resistant. Thus, the structure and function of FV and its interaction with APC are highly conserved across mammalian species.

scholarly journals His···Asp Catalytic Dyad of Ribonuclease A:  Structure and Function of the Wild-Type, D121N, and D121A Enzymes†

Biochemistry ◽  
1998 ◽  
Vol 37 (25) ◽  
pp. 8886-8898 ◽  
Author(s):  
L. Wayne Schultz ◽  
David J. Quirk ◽  
Ronald T. Raines
Keyword(s):  
Ribonuclease A ◽  
Structure And Function ◽  
Wild Type ◽  
And Function ◽  
Catalytic Dyad

scholarly journals Structure and function of wild-type and subunit-depleted photosystem I in Synechocystis

2018 ◽  
Vol 1859 (9) ◽  
pp. 645-654 ◽  
Author(s):  
Tirupathi Malavath ◽  
Ido Caspy ◽  
Sigal Y. Netzer-El ◽  
Daniel Klaiman ◽  
Nathan Nelson
Keyword(s):  
Photosystem I ◽  
Structure And Function ◽  
Wild Type ◽  
And Function

scholarly journals Kindlin-2 suppresses transcription factor GATA4 through interaction with SUV39H1 to attenuate hypertrophy

2019 ◽  
Vol 10 (12) ◽  
Author(s):  
Lihua Qi ◽  
Xiaochun Chi ◽  
Xi Zhang ◽  
Xueqian Feng ◽  
Wenhui Chu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Pathological Process ◽  
Structure And Function ◽  
Wild Type ◽  
Cardiac Tissues ◽  
Targeted Deletion ◽  
Progressive Heart Failure ◽  
Pathological Hypertrophy ◽  
And Function

AbstractKindlin-2 plays an important role in the regulation of cardiac structure and function. Depletion of Kindlin-2 contributes to cardiac hypertrophy and progressive heart failure, however, the precise mechanisms involved in this process remain unclear. GATA4 is a critical transcription factor in regulating cardiogenesis. We found that Kindlin-2 suppresses the expression of GATA4 through binding to its promoter and prevents cardiomyocytes from hypertrophy induced by isoproterenol (ISO) treatment. Mechanistically, Kindlin-2 interacts with histone methyltransferase SUV39H1 and recruits it to GATA4 promoter leading to the occupancy of histone H3K9 di- and tri-methylation. Furthermore, to confirm the function of Kindlin-2 in vivo, we generated mice with targeted deletion of cardiac Kindlin-2. We found that 6-month-old Kindlin-2 cKO mice have developed hypertrophic cardiomyopathy and that this pathological process can be accelerated by ISO-treatment. GATA4 expression was markedly activated in cardiac tissues of Kindlin-2 cKO mice compared to wild-type animals. Collectively, our data revealed that Kindlin-2 suppresses GATA4 expression by triggering histone H3K9 methylation in part and protects heart from pathological hypertrophy.

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