scholarly journals Diversity in Starvation Survival Strategies and Outcomes among Heterotrophic Proteobacteria

2021 ◽  
pp. 1-17
Author(s):  
Megan Bergkessel ◽  
Laurent Delavaine
Keyword(s):  
Regulatory Networks ◽  
Cell Envelope ◽  
Carbon Starvation ◽  
Survival Strategies ◽  
Model Organisms ◽  
Electrochemical Gradient ◽  
Bacterial Strains ◽  
Free Living ◽  
Starvation Survival ◽  
Cellular Integrity

Heterotrophic Proteobacteria are versatile opportunists that have been extensively studied as model organisms in the laboratory, as both pathogens and beneficial symbionts of plants and animals, and as ubiquitous organisms found free-living in many environments. Succeeding in these niches requires an ability to persist for potentially long periods of time in growth-arrested states when essential nutrients become limiting. The tendency of these bacteria to grow in dense biofilm communities frequently leads to the development of steep nutrient gradients and deprivation of interior cells even when the environment is nutrient rich. Surviving within host environments also likely requires tolerating growth arrest due to the host limiting access to nutrients and transitioning between hosts may require a period of survival in a nutrient-poor environment. Interventions to maximise plant-beneficial activities and minimise infections by bacteria will require a better understanding of metabolic and regulatory networks that contribute to starvation survival, and how these networks function in diverse organisms. Here we focus on carbon starvation as a growth-arresting condition that limits availability not only of substrates for biosynthesis but also of energy for ongoing maintenance of the electrochemical gradient across the cell envelope and cellular integrity. We first review models for studying bacterial starvation and known strategies that contribute to starvation survival<i>.</i> We then present the results of a survey of carbon starvation survival strategies and outcomes in ten bacterial strains, including representatives from the orders Enterobacterales and Pseudomonadales (both Gammaproteobacteria) and Burkholderiales (Betaproteobacteria). Finally, we examine differences in gene content between the highest and lowest survivors to identify metabolic and regulatory adaptations that may contribute to differences in starvation survival.

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.

scholarly journals Pathovar Transcriptomes

mSystems ◽  
2017 ◽  
Vol 2 (4) ◽  
Author(s):  
Amy Platenkamp ◽  
Jay L. Mellies
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Regulatory Networks ◽  
Virulence Gene ◽  
Model System ◽  
Genomic Sequences ◽  
Bacterial Strains ◽  
Content Type ◽  
Virulence Gene Expression ◽  
Link Type

ABSTRACT Archetypal pathogenic bacterial strains are often used to elucidate regulatory networks of an entire pathovar, which encompasses multiple lineages and phylogroups. With enteropathogenic Escherichia coli (EPEC) as a model system, Hazen and colleagues (mSystems 6:e00024-17, 2017, https://doi.org/10.1128/mSystems.00024-17 ) used 9 isolates representing 8 lineages and 3 phylogroups to find that isolates with similar genomic sequences exhibit similarities in global transcriptomes under conditions of growth in medium that induces virulence gene expression, and they found variation among individual isolates. Archetypal pathogenic bacterial strains are often used to elucidate regulatory networks of an entire pathovar, which encompasses multiple lineages and phylogroups. With enteropathogenic Escherichia coli (EPEC) as a model system, Hazen and colleagues (mSystems 6:e00024-17, 2017, https://doi.org/10.1128/mSystems.00024-17 ) used 9 isolates representing 8 lineages and 3 phylogroups to find that isolates with similar genomic sequences exhibit similarities in global transcriptomes under conditions of growth in medium that induces virulence gene expression. They also found variation among individual isolates. Their work illustrates the importance of moving beyond observing regulatory phenomena of a limited number of regulons in a few archetypal strains, with the possibility of correlating clinical symptoms to key transcriptional pathways across lineages and phylogroups.

scholarly journals Phyletic distribution and diversification of the Phage Shock Protein stress response system in bacteria and archaea

2021 ◽  
Author(s):  
Philipp F. Popp ◽  
Vadim M. Gumerov ◽  
Ekaterina P. Andrianova ◽  
Lisa Bewersdorf ◽  
Thorsten Mascher ◽  
...  
Keyword(s):  
Stress Response ◽  
Large Scale ◽  
Cell Envelope ◽  
Model Organisms ◽  
Microbial World ◽  
Natural Classification ◽  
Response System ◽  
Core Proteins ◽  
Envelope Stress

AbstractThe bacterial cell envelope is an essential structure that protects the cell from environmental threats, while simultaneously serving as communication interface and diffusion barrier. Therefore, maintaining cell envelope integrity is of vital importance for all microorganisms. Not surprisingly, evolution has shaped conserved protection networks that connect stress perception, transmembrane signal transduction and mediation of cellular responses upon cell envelope stress. The phage shock protein (PSP) stress response is one of such conserved protection networks. Most of the knowledge about the Psp response comes from studies in the Gram-negative model bacterium, Escherichia coli where the Psp system consists of several well-defined protein components. Homologous systems were identified in representatives of Proteobacteria, Actinobacteria, and Firmicutes; however, the Psp system distribution in the microbial world remains largely unknown. By carrying out a large-scale, unbiased comparative genomics analysis, we found components of the Psp system in many bacterial and archaeal phyla and demonstrated that the PSP system deviates dramatically from the proteobacterial prototype. Two of its core proteins, PspA and PspC, have been integrated in various (often phylum-specifically) conserved protein networks during evolution. Based on protein sequence and gene neighborhood analyses of pspA and pspC homologs, we built a natural classification system of PSP networks in bacteria and archaea. We performed a comprehensive in vivo protein interaction screen for the PSP network newly identified in the Gram-positive model organism Bacillus subtilis and found a strong interconnected PSP response system, illustrating the validity of our approach. Our study highlights the diversity of PSP organization and function across many bacterial and archaeal phyla and will serve as foundation for future studies of this envelope stress response beyond model organisms.

Molecular and physiological comparison ofAzospirillumspp. isolated fromRhizoctonia solanimycelia, wheat rhizosphere, and human skin wounds

2004 ◽  
Vol 50 (4) ◽  
pp. 291-297 ◽  
Author(s):  
Michael F Cohen ◽  
Xiang Y Han ◽  
Mark Mazzola
Keyword(s):  
Rhizoctonia Solani ◽  
Azospirillum Brasilense ◽  
Type Strain ◽  
Apple Orchard ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Free Living ◽  
Root Pathogen ◽  
Wide Range ◽  
Orchard Soil

Four phenotypically similar bacterial strains isolated from fungal, plant, and human sources were identified as Azospirillum species. Strains RC1 and LOD4 were isolated from the mycelium of the apple root pathogen Rhizoctonia solani AG 5 and from the rhizosphere of wheat grown in apple orchard soil, respectively. Strains C610 and F4626 isolated from human wounds were previously misclassified as Roseomonas genomospecies 3 and 6. All four strains demonstrated close similarities in 16S rRNA gene sequences, having [Formula: see text]97% identity to Azospirillum brasilense type strain ATCC 29145 and <90% identity to Roseomonas gilardii, the Roseomonas type strain. Extensive phenotypic similarities among the four strains included the ability of free-living cells to fix N2. Cells of strains RC1, LOD4, and C610 but not of strain F4626 could be induced to flocculate by incubation with 10 mmol·L–1glycerol or fructose in medium containing 0.5 mmol·L–1NO3–. Our results indicate a wide range of potential sources for Azospirillum spp. with the isolation of Azospirillum spp. from human wounds warranting further investigation.Key words: Azospirillum brasilense, Roseomonas fauriae, flocculation, Rhizoctonia solani.

scholarly journals Archaeal cell biology: diverse functions of tubulin-like cytoskeletal proteins at the cell envelope

2018 ◽  
Vol 2 (4) ◽  
pp. 547-559 ◽  
Author(s):  
Yan Liao ◽  
Solenne Ithurbide ◽  
Roshali T. de Silva ◽  
Susanne Erdmann ◽  
Iain G. Duggin
Keyword(s):  
Cell Biology ◽  
Shape Control ◽  
Cell Envelope ◽  
Light And Electron Microscopy ◽  
Halophilic Archaea ◽  
Cytoskeletal Proteins ◽  
Model Organisms ◽  
Full Spectrum ◽  
Peptidoglycan Cell Wall ◽  
Domains Of Life

The tubulin superfamily of cytoskeletal proteins is widespread in all three domains of life — Archaea, Bacteria and Eukarya. Tubulins build the microtubules of the eukaryotic cytoskeleton, whereas members of the homologous FtsZ family construct the division ring in prokaryotes and some eukaryotic organelles. Their functions are relatively poorly understood in archaea, yet these microbes contain a remarkable diversity of tubulin superfamily proteins, including FtsZ for division, a newly described major family called CetZ that is involved in archaeal cell shape control, and several other divergent families of unclear function that are implicated in a variety of cell envelope-remodelling contexts. Archaeal model organisms, particularly halophilic archaea such as Haloferax volcanii, have sufficiently developed genetic tools and we show why their large, flattened cells that are capable of controlled differentiation are also well suited to cell biological investigations by live-cell high-resolution light and electron microscopy. As most archaea only have a glycoprotein lattice S-layer, rather than a peptidoglycan cell wall like bacteria, the activity of the tubulin-like cytoskeletal proteins at the cell envelope is expected to vary significantly, and may involve direct membrane remodelling or directed synthesis or insertion of the S-layer protein subunits. Further studies of archaeal cell biology will provide fresh insight into the evolution of cells and the principles in common to their fundamental activities across the full spectrum of cellular life.

LOOKING FOR EVIDENCE OF DIFFERENTIATION AND COOPERATION: NATURAL MEASURES FOR THE STUDY OF EVOLUTION OF MULTICELLULARITY

2009 ◽  
Vol 12 (03) ◽  
pp. 255-271
Author(s):  
MORITZ BUCK ◽  
CHRYSTOPHER L. NEHANIV
Keyword(s):  
Artificial Life ◽  
Regulatory Networks ◽  
Single Cells ◽  
Genetic Regulatory Networks ◽  
Free Living ◽  
Evolutionary Transitions ◽  
A Cell ◽  
Communication Ability ◽  
Natural Measures ◽  
The Impact

The understanding of the evolutionary transitions is a major area of research in artificial life and in biology. We follow an artificial life approach to investigate these phenomena, using a system inspired by Anabaena cyanobacteria (which exhibit rudimentary multicellular differentiation and cooperation) in order to look for evidence of emerging differentiation and multicellular cooperation in colonies of individual cells.We first evolve single free-living cells with the help of a Genetic Algorithm (GA). These cells are controlled with genetic regulatory networks. The single cells are evolved to each perform both of two tasks: an abstraction of house-keeping metabolism and a reproductive cycle. Once such a cell was evolved with the GA, the cell is used to seed the growth of a multicellular filamentous colony, whose constituent cells continue to reproduce and evolve. Two types of colonies generated from the seed cell are studied: one with intercellular communication ability and one without.We introduce and apply new measures for assessing the impact of multicellular interaction on individual reproduction and on life span.The conclusion of these studies shows that the colony with the ability to communicate shows, with the help of our new measures, behaviors that hint at the emergence of early cooperation.

Research on Improvement of Nitrogenase Activity of Free-Living Nitrogen-Fixing Bacteria Using DBD Plasma

2013 ◽  
Vol 671-674 ◽  
pp. 2674-2678 ◽  
Author(s):  
Yan Yun Zhu ◽  
Xiao Li Zhu ◽  
Fang She Yang
Keyword(s):  
Rhizosphere Soil ◽  
Barrier Discharge ◽  
Nitrogenase Activity ◽  
Nitrogen Fixing ◽  
Bacterial Strains ◽  
Dbd Plasma ◽  
Nitrogen Fixing Bacteria ◽  
Free Living ◽  
Reduction Assay ◽  
Rrna Sequencing

Nitrogen-fixing bacteria were screened from the rhizosphere soil of plants in Shaanxi in China. 36 free-living nitrogen-fixing bacterial strains were isolated and their nitrogenase activity were determined by acetylene reduction assay (ARA), two strains named FLNB03 and FLNB09 with higher nitrogenase activity were isolated and identified by 16S rRNA sequencing. The datum showed that FLNB03 was similar to Acinetobacter and their similarity reached 99%, FLNB09 was similar to Agrobacterium sp. and their similarity reached 99%. Then both of them were treated using Dielectric Barrier Discharge (DBD) plasma for mutation and their mutants called FLNB03-2 and FLNB09-3 were obtained. The nitrogenase activity of FLNB03-2 was 0.61±0.10 nmol•107cfu-1•h-1, and that of FLNB09-3 was 0.40±0.05 nmol•107cfu-1•h-1, their nitrogenase activity increased by 22.00% and 14.29% than their original bacteria respectively. FLNB03-2 and FLNB09-3 might be used as microbial fertilizer.

scholarly journals Identification of Bacterial Proteins Mediating the Interactions Between Pseudomonas putida UW4 and Brassica napus (Canola)

2009 ◽  
Vol 22 (6) ◽  
pp. 686-694 ◽  
Author(s):  
Zhenyu Cheng ◽  
Jin Duan ◽  
Youai Hao ◽  
Brendan J. McConkey ◽  
Bernard R. Glick
Keyword(s):  
Pseudomonas Putida ◽  
Root Exudates ◽  
Translational Regulation ◽  
Cell Envelope ◽  
Effective Means ◽  
Wild Type ◽  
Bacterial Strains ◽  
Uncharacterized Protein ◽  
Altered Expression ◽  
Bacterial Interactions

The influence of canola root exudates on the proteome of Pseudomonas putida UW4 and the mutant strain P. putida UW4/AcdS–, which lacks a functional 1-aminocyclopropane-1-carboxylate deaminase gene, was examined using two-dimensional difference in-gel electrophoresis. Seventy-two proteins with significantly altered expression levels in the presence of canola root exudates were identified by mass spectrometry. Many of these proteins are involved in nutrient transport and utilization, cell envelope synthesis, and transcriptional or translational regulation and, hence, may play important roles in plant–bacterial interactions. Four proteins showing large changes in expression in response to canola root exudates in both the wild-type and mutant strains of P. putida UW4 (i.e., outer membrane protein F, peptide deformylase, transcription regulator Fis family protein, and a previously uncharacterized protein) were both overexpressed and disrupted in P. putida UW4 in an effort to better understand their functions. Functional studies of these modified strains revealed significantly enhanced or inhibited plant-growth-promoting abilities compared with the wild-type P. putida UW4, in agreement with the suggested involvement of three of these four proteins in plant–bacterial interactions. The work reported here suggests strategies to both identify potential antibacterial agents and develop bacterial strains that might be useful adjuncts to agriculture. This approach may be an effective means of identifying key proteins mediating the interactions of bacteria with their rhizosphere environment.

In vitro inhibition of nonsymbiotic nitrogen-fixing bacteria by rhizosphere actinomycetes associated with grasses

1982 ◽  
Vol 28 (6) ◽  
pp. 705-709 ◽  
Author(s):  
D. A. Zuberer ◽  
Mark Roth
Keyword(s):  
Antibiotic Production ◽  
Nitrogen Fixing ◽  
Diazotrophic Bacteria ◽  
Bacterial Strains ◽  
Free Living ◽  
Vitro Assay ◽  
Genus Streptomyces ◽  
Central Texas ◽  
Actinomycete Isolate

Eighty-five isolates of actinomycetes were obtained from the rhizospheres of 10 indigenous grasses of central Texas. Of these, 10 were classified as members of the genus Nocardia; the remainder were members of the genus Streptomyces. To determine whether antibiotic production might be a significant factor in the establishment of associative symbioses between grasses and diazotrophic bacteria, 12 strains of free-living nitrogen-fixing bactria were cross streaked against each actinomycete isolate. This in vitro assay indicated that 78% of the 85 isolates were antagonistic to at least one of the 12 nitrogen-fixing bacterial strains.

scholarly journals A novel flatworm-specific gene family implicated in reproduction in Macrostomum lignano

2017 ◽  
Author(s):  
Magda Grudniewska ◽  
Stijn Mouton ◽  
Margriet Grelling ◽  
Anouk H. G. Wolters ◽  
Jeroen Kuipers ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Stem Cells ◽  
Gene Family ◽  
Model Organisms ◽  
Future Research ◽  
Specific Gene ◽  
Free Living ◽  
Ultrastructural Studies ◽  
Conserved Genes ◽  
High Fraction

AbstractFree-living flatworms, such as the planarian Schmidtea mediterranea, are extensively used as model organisms to study stem cells and regeneration. The majority of studies in planarians so far focused on broadly conserved genes. However, investigating what makes these animals different might be equally informative for understanding its biology. Here, we present a re-analysis of neoblast and germline transcriptional signatures in the flatworm M. lignano and combine it with the whole-animal electron microscopy atlas (nanotomy) as a reference platform for ultrastructural studies in M. lignano. We show that germline-enriched genes have a high fraction of flatworm-specific genes and identify Mlig-sperm1 gene as a member of a novel gene family conserved only in free-living flatworms and essential for producing healthy spermatozoa. This work demonstrates that investigation of flatworm-specific genes is crucial for understanding flatworm biology and establishes a basis for future research in this direction in M. lignano.

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