scholarly journals Gene-centric intra- and inter-clade recombination in a context ofEsche-richia colisubpopulations

2017 ◽  
Author(s):  
Yu Kang ◽  
Xing Shi ◽  
Lina Yuan ◽  
Yanan Chu ◽  
Fei Chen ◽  
...  
Keyword(s):  
Early Stage ◽  
Critical Role ◽  
Ecological Niches ◽  
Phylogenetic Distance ◽  
Bacterial Genomes ◽  
Genetic Barrier ◽  
Ecological Fitness ◽  
E Coli ◽  
Genome Wide ◽  
Species Evolution

ABSTRACTRecombination is one of the most important mechanisms of prokaryotic species evolution but its exact roles are still in debate. Here we try to infer genome-wide recombination events within a species uti-lizing a dataset of 104 complete genomes ofEscherichia colifrom diverse origins, among which 45 from world-wide animal-hosts are in-house sequenced using SMRT (single-molecular real time) technology.Two major clades are identified based on evidences of ecological and physiological characteristics, as well as distinct genomic features implying scarce inter-clade genetic exchange. By comparing the synteny of identical fragments genome-widely searched for each genome pair, we achieve a fine-scale map of re-combination within the population. The recombination is rather extensive within clade, which is able to break linkages between genes but does not interrupt core genome framework and primary metabolic port-folios possibly due to natural selection for physiological compatibility and ecological fitness. Meanwhile,the recombination between clades declines drastically as the phylogenetic distance increases, generally 10-fold reduced than those of the intra-clade, which establishes genetic barrier between clades. These empirical data of recombination suggest its critical role in the early stage of speciation, where recombina-tion rate differs according to phylogentic distance. The extensive intra-clade recombination coheres sister strains into a quasi-sexual group and optimizes genes or alleles to streamline physiological activities,whereas shapely declined inter-clade recombination split the population into clades adaptive to divergent ecological niches.Significance StatementRoles of recombination in species evolution have been debated for decades due to difficulties in inferring recombination events during the early stage of speciation, especially when recombination is always complicated by frequent gene transfer events of bacterial genomes. Based on 104 high-quality completeE. coligenomes, we infer gene-centric dynamics of recombination in the formation of twoE. coliclades or subpopulations, and recombination is found to be rather intensive in a within-clade fashion, which forces them to be quasi-sexual. The recombination events can be mapped among individual genomes in the context of genes and their variations; decreased between-clade and increased intra-claderecombination engender a genetic barrier that further encourages clade-specific secondary metabolic portfolios for better environmental adaptation. Recombination is thus a major force that accelerates bacterial evolution to fit ecological diversity.

A fine-scale map of genome-wide recombination in divergent Escherichia coli population

2020 ◽  
Author(s):  
Yu Kang ◽  
Lina Yuan ◽  
Xing Shi ◽  
Yanan Chu ◽  
Zilong He ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Mechanisms ◽  
Early Stage ◽  
Critical Role ◽  
Prokaryotic Genome ◽  
Ecological Niches ◽  
Phylogenetic Distance ◽  
Fine Scale ◽  
Ecological Fitness ◽  
Genome Wide

Abstract Recombination is one of the most important molecular mechanisms of prokaryotic genome evolution, but its exact roles are still in debate. Here we try to infer genome-wide recombination within a species, utilizing a dataset of 149 complete genomes of Escherichia coli from diverse animal hosts and geographic origins, including 45 in-house sequenced with the single-molecular real-time platform. Two major clades identified based on physiological, clinical and ecological characteristics form distinct genetic lineages based on scarcity of interclade gene exchanges. By defining gene-based syntenies for genomic segments within and between the two clades, we build a fine-scale recombination map for this representative global E. coli population. The map suggests extensive within-clade recombination that often breaks physical linkages among individual genes but seldom interrupts the structure of genome organizational frameworks as well as primary metabolic portfolios supported by the framework integrity, possibly due to strong natural selection for both physiological compatibility and ecological fitness. In contrast, the between-clade recombination declines drastically when phylogenetic distance increases to the extent where a 10-fold reduction can be observed, establishing a firm genetic barrier between clades. Our empirical data suggest a critical role for such recombination events in the early stage of speciation where recombination rate is associated with phylogenetic distance in addition to sequence and gene variations. The extensive intraclade recombination binds sister strains into a quasisexual group and optimizes genes or alleles to streamline physiological activities, whereas the sharply declined interclade recombination split the population into clades adaptive to divergent ecological niches.

Sequence of Colonization Determines the Composition of Mixed Biofilms by Escherichia coli O157:H7 and O111:H8 Strains†

2015 ◽  
Vol 78 (8) ◽  
pp. 1554-1559 ◽  
Author(s):  
RONG WANG ◽  
NORASAK KALCHAYANAND ◽  
JAMES L. BONO
Keyword(s):  
Escherichia Coli ◽  
Foodborne Pathogens ◽  
Early Stage ◽  
Critical Role ◽  
The United States ◽  
Food Samples ◽  
E Coli ◽  
Cell Percentage ◽  
Composition And Structure ◽  
Biofilm Development

Bacterial biofilms are one of the potential sources of cross-contamination in food processing environments. Shiga toxin–producing Escherichia coli (STEC) O157:H7 and O111:H8 are important foodborne pathogens capable of forming biofilms, and the coexistence of these two STEC serotypes has been detected in various food samples and in multiple commercial meat plants throughout the United States. Here, we investigated how the coexistence of these two STEC serotypes and their sequence of colonization could affect bacterial growth competition and mixed biofilm development. Our data showed that E. coli O157:H7 strains were able to maintain a higher cell percentage in mixed biofilms with the co-inoculated O111:H8 companion strains, even though the results of planktonic growth competition were strain dependent. On solid surfaces with preexisting biofilms, the sequence of colonization played a critical role in determining the composition of the mixed biofilms because early stage precolonization significantly affected the competition results between the E. coli O157:H7 and O111:H8 strains. The precolonizer of either serotype was able to outgrow the other serotype in both planktonic and biofilm phases. The competitive interactions among the various STEC serotypes would determine the composition and structure of the mixed biofilms as well as their potential risks to food safety and public health, which is largely influenced by the dominant strains in the mixtures. Thus, the analysis of mixed biofilms under various conditions would be of importance to determine the nature of mixed biofilms composed of multiple microorganisms and to help implement the most effective disinfection operations accordingly.

scholarly journals Molecular archaeology of theEscherichia coligenome

1998 ◽  
Vol 95 (16) ◽  
pp. 9413-9417 ◽  
Author(s):  
Jeffrey G. Lawrence ◽  
Howard Ochman
Keyword(s):  
Escherichia Coli ◽  
Complete Sequence ◽  
Lateral Transfer ◽  
Ecological Niches ◽  
Bacterial Genomes ◽  
Strain Mg1655 ◽  
Genetic Transfer ◽  
E Coli

The availability of the complete sequence ofEscherichia colistrain MG1655 provides the first opportunity to assess the overall impact of horizontal genetic transfer on the evolution of bacterial genomes. We found that 755 of 4,288 ORFs (547.8 kb) have been introduced into theE. coligenome in at least 234 lateral transfer events since this species diverged from theSalmonellalineage 100 million years (Myr) ago. The average age of introduced genes was 14.4 Myr, yielding a rate of transfer 16 kb/Myr/lineage since divergence. Although most of the acquired genes subsequently were deleted, the sequences that have persisted (≈18% of the current chromosome) have conferred properties permittingE. colito explore otherwise unreachable ecological niches.

scholarly journals Genome-wide dissection reveals diverse pathogenic roles of bacterial Tc toxins

2021 ◽  
Vol 17 (2) ◽  
pp. e1009102
Author(s):  
Nan Song ◽  
Lihong Chen ◽  
Zhemin Zhou ◽  
Xingmei Ren ◽  
Bo Liu ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Critical Role ◽  
Host Cells ◽  
Bacterial Genomes ◽  
Biological Pest Control ◽  
Core Domain ◽  
Hypervariable Regions ◽  
Specific Distribution ◽  
Genome Wide ◽  
Wide Range

Tc toxins were originally identified in entomopathogenic bacteria, which are important as biological pest control agents. Tc toxins are heteromeric exotoxins composed of three subunit types, TcA, TcB, and TcC. The C-terminal portion of the TcC protein encodes the actual toxic domain, which is translocated into host cells by an injectosome nanomachine comprising the other subunits. Currently the pathogenic roles and distribution of Tc toxins among different bacterial genera remain unclear. Here we have performed a comprehensive genome-wide analysis, and established a database that includes 1,608 identified Tc loci containing 2,528 TcC proteins in 1,421 Gram-negative and positive bacterial genomes. Our findings indicate that TcCs conform to the architecture of typical polymorphic toxins, with C-terminal hypervariable regions (HVR) encoding more than 100 different classes of putative toxic domains, most of which have not been previously recognized. Based on further analysis of Tc loci in the genomes of all Salmonella and Yersinia strains in EnteroBase, a “two-level” evolutionary dynamics scenario is proposed for TcC homologues. This scenario implies that the conserved TcC RHS core domain plays a critical role in the taxonomical specific distribution of TcC HVRs. This study provides an extensive resource for the future development of Tc toxins as valuable agrochemical tools. It furthermore implies that Tc proteins, which are encoded by a wide range of pathogens, represent an important versatile toxin superfamily with diverse pathogenic mechanisms.

Genome-wide screen identifies curli amyloid fibril as a bacterial component promoting host neurodegeneration

2021 ◽  
Author(s):  
CHENYIN WANG ◽  
Chun Yin Lau ◽  
Fuqiang Ma ◽  
Chaogu Zheng
Keyword(s):  
Amyloid Fibril ◽  
Critical Role ◽  
Neuroblastoma Cells ◽  
Human Neuroblastoma ◽  
E Coli ◽  
C Elegans ◽  
Host Interaction ◽  
Genome Wide ◽  
A Genome ◽  
Bacterial Genes

Growing evidence indicate that gut microbiota play a critical role in regulating the progression of neurodegenerative diseases, such as Parkinson's disease (PD). The molecular mechanism underlying such microbe-host interaction is unclear. In this study, by feeding C. elegans expressing human α-syn with E. coli knockout mutants, we conducted a genome-wide screen to identify bacterial genes that promote host neurodegeneration. The screen yielded 38 genes that fall into several genetic pathways, including curli formation, lipopolysaccharide assembly, adenosylcobalamin biosynthesis among others. We then focused on the curli amyloid fibril and found that genetically deleting or pharmacologically inhibiting the curli major subunit CsgA in E. coli reduced α-syn-induced neuronal death, restored mitochondrial health, and improved neuronal functions. CsgA secreted by the bacteria colocalized with α-syn inside neurons and promoted α-syn aggregation through cross-seeding. Similarly, curli also promoted neurodegeneration in C. elegans models of AD, ALS, and HD and in human neuroblastoma cells.

scholarly journals Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cuili Pan ◽  
Zhaoxiong Lei ◽  
Shuzhe Wang ◽  
Xingping Wang ◽  
Dawei Wei ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Adipocyte Differentiation ◽  
Bos Taurus ◽  
Adipogenic Differentiation ◽  
Critical Role ◽  
Bos Indicus ◽  
Specific Expression ◽  
Genome Wide ◽  
A Genome

Abstract Background Cyclin-dependent kinases (CDKs) are protein kinases regulating important cellular processes such as cell cycle and transcription. Many CDK genes also play a critical role during adipogenic differentiation, but the role of CDK gene family in regulating bovine adipocyte differentiation has not been studied. Therefore, the present study aims to characterize the CDK gene family in bovine and study their expression pattern during adipocyte differentiation. Results We performed a genome-wide analysis and identified a number of CDK genes in several bovine species. The CDK genes were classified into 8 subfamilies through phylogenetic analysis. We found that 25 bovine CDK genes were distributed in 16 different chromosomes. Collinearity analysis revealed that the CDK gene family in Bos taurus is homologous with Bos indicus, Hybrid-Bos taurus, Hybrid Bos indicus, Bos grunniens and Bubalus bubalis. Several CDK genes had higher expression levels in preadipocytes than in differentiated adipocytes, as shown by RNA-seq analysis and qPCR, suggesting a role in the growth of emerging lipid droplets. Conclusion In this research, 185 CDK genes were identified and grouped into eight distinct clades in Bovidae, showing extensively homology. Global expression analysis of different bovine tissues and specific expression analysis during adipocytes differentiation revealed CDK4, CDK7, CDK8, CDK9 and CDK14 may be involved in bovine adipocyte differentiation. The results provide a basis for further study to determine the roles of CDK gene family in regulating adipocyte differentiation, which is beneficial for beef quality improvement.

scholarly journals Genome-wide CRISPR/Cas9 screening identifies CARHSP1 responsible for radiation resistance in glioblastoma

2021 ◽  
Vol 12 (8) ◽  
Author(s):  
Guo-dong Zhu ◽  
Jing Yu ◽  
Zheng-yu Sun ◽  
Yan Chen ◽  
Hong-mei Zheng ◽  
...  
Keyword(s):  
Cold Shock ◽  
Mrna Level ◽  
Critical Role ◽  
Inflammatory Signaling ◽  
Heat Stable ◽  
Genome Wide ◽  
Attractive Therapeutic Target ◽  
Heat Stable Protein ◽  
Signaling Activation ◽  
Shock Proteins

AbstractGlioblastomas (GBM) is the most common primary malignant brain tumor, and radiotherapy plays a critical role in its therapeutic management. Unfortunately, the development of radioresistance is universal. Here, we identified calcium-regulated heat-stable protein 1 (CARHSP1) as a critical driver for radioresistance utilizing genome-wide CRISPR activation screening. This is a protein with a cold-shock domain (CSD)-containing that is highly similar to cold-shock proteins. CARHSP1 mRNA level was upregulated in irradiation-resistant GBM cells and knockdown of CARHSP1 sensitized GBM cells to radiotherapy. The high expression of CARHSP1 upon radiation might mediate radioresistance by activating the inflammatory signaling pathway. More importantly, patients with high levels of CARHSP1 had poorer survival when treated with radiotherapy. Collectively, our findings suggested that targeting the CARHSP1/TNF-α inflammatory signaling activation induced by radiotherapy might directly affect radioresistance and present an attractive therapeutic target for GBM, particularly for patients with high levels of CARHSP1.

scholarly journals High-throughput microbioreactor provides a capable tool for early stage bioprocess development

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mathias Fink ◽  
Monika Cserjan-Puschmann ◽  
Daniela Reinisch ◽  
Gerald Striedner
Keyword(s):  
High Throughput ◽  
Process Development ◽  
Early Stage ◽  
Explanatory Power ◽  
Batch Mode ◽  
E Coli ◽  
Speed Up ◽  
Bioreactor System ◽  
Cell Densities ◽  
Microbial Systems

AbstractTremendous advancements in cell and protein engineering methodologies and bioinformatics have led to a vast increase in bacterial production clones and recombinant protein variants to be screened and evaluated. Consequently, an urgent need exists for efficient high-throughput (HTP) screening approaches to improve the efficiency in early process development as a basis to speed-up all subsequent steps in the course of process design and engineering. In this study, we selected the BioLector micro-bioreactor (µ-bioreactor) system as an HTP cultivation platform to screen E. coli expression clones producing representative protein candidates for biopharmaceutical applications. We evaluated the extent to which generated clones and condition screening results were transferable and comparable to results from fully controlled bioreactor systems operated in fed-batch mode at moderate or high cell densities. Direct comparison of 22 different production clones showed great transferability. We observed the same growth and expression characteristics, and identical clone rankings except one host-Fab-leader combination. This outcome demonstrates the explanatory power of HTP µ-bioreactor data and the suitability of this platform as a screening tool in upstream development of microbial systems. Fast, reliable, and transferable screening data significantly reduce experiments in fully controlled bioreactor systems and accelerate process development at lower cost.

scholarly journals Global versus Local Regulatory Roles for Lrp-Related Proteins: Haemophilus influenzae as a Case Study

2001 ◽  
Vol 183 (13) ◽  
pp. 4004-4011 ◽  
Author(s):  
Devorah Friedberg ◽  
Michael Midkiff ◽  
Joseph M. Calvo
Keyword(s):  
Amino Acid ◽  
Haemophilus Influenzae ◽  
Regulatory Protein ◽  
Enteric Bacteria ◽  
Regulatory Role ◽  
Regulatory Function ◽  
Ecological Niches ◽  
E Coli ◽  
Sequence Identity ◽  
Related Proteins

ABSTRACT Lrp (leucine-responsive regulatory protein) plays a global regulatory role in Escherichia coli, affecting expression of dozens of operons. Numerous lrp-related genes have been identified in different bacteria and archaea, includingasnC, an E. coli gene that was the first reported member of this family. Pairwise comparisons of amino acid sequences of the corresponding proteins shows an average sequence identity of only 29% for the vast majority of comparisons. By contrast, Lrp-related proteins from enteric bacteria show more than 97% amino acid identity. Is the global regulatory role associated withE. coli Lrp limited to enteric bacteria? To probe this question we investigated LrfB, an Lrp-related protein fromHaemophilus influenzae that shares 75% sequence identity with E. coli Lrp (highest sequence identity among 42 sequences compared). A strain of H. influenzae having anlrfB null allele grew at the wild-type growth rate but with a filamentous morphology. A comparison of two-dimensional (2D) electrophoretic patterns of proteins from parent and mutant strains showed only two differences (comparable studies withlrp + and lrp E. coli strains by others showed 20 differences). The abundance of LrfB in H. influenzae, estimated by Western blotting experiments, was about 130 dimers per cell (compared to 3,000 dimers per E. colicell). LrfB expressed in E. coli replaced Lrp as a repressor of the lrp gene but acted only to a limited extent as an activator of the ilvIH operon. Thus, although LrfB resembles Lrp sufficiently to perform some of its functions, its low abundance is consonant with a more local role in regulating but a few genes, a view consistent with the results of the 2D electrophoretic analysis. We speculate that an Lrp having a global regulatory role evolved to help enteric bacteria adapt to their ecological niches and that it is unlikely that Lrp-related proteins in other organisms have a broad regulatory function.

scholarly journals A Genome-Wide Screen in Saccharomyces cerevisiae Reveals a Critical Role for Oxidative Phosphorylation in Cellular Tolerance to Lithium Hexafluorophosphate

Cells ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 888
Author(s):  
Xuejiao Jin ◽  
Jie Zhang ◽  
Tingting An ◽  
Huihui Zhao ◽  
Wenhao Fu ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Oxidative Phosphorylation ◽  
Cellular Response ◽  
Critical Role ◽  
Lithium Ion ◽  
Deletion Mutants ◽  
High Concentration ◽  
Genome Wide ◽  
A Genome ◽  
Lithium Hexafluorophosphate

Lithium hexafluorophosphate (LiPF6) is one of the leading electrolytes in lithium-ion batteries, and its usage has increased tremendously in the past few years. Little is known, however, about its potential environmental and biological impacts. In order to improve our understanding of the cytotoxicity of LiPF6 and the specific cellular response mechanisms to it, we performed a genome-wide screen using a yeast (Saccharomyces cerevisiae) deletion mutant collection and identified 75 gene deletion mutants that showed LiPF6 sensitivity. Among these, genes associated with mitochondria showed the most enrichment. We also found that LiPF6 is more toxic to yeast than lithium chloride (LiCl) or sodium hexafluorophosphate (NaPF6). Physiological analysis showed that a high concentration of LiPF6 caused mitochondrial damage, reactive oxygen species (ROS) accumulation, and ATP content changes. Compared with the results of previous genome-wide screening for LiCl-sensitive mutants, we found that oxidative phosphorylation-related mutants were specifically hypersensitive to LiPF6. In these deletion mutants, LiPF6 treatment resulted in higher ROS production and reduced ATP levels, suggesting that oxidative phosphorylation-related genes were important for counteracting LiPF6-induced toxicity. Taken together, our results identified genes specifically involved in LiPF6-modulated toxicity, and demonstrated that oxidative stress and ATP imbalance maybe the driving factors in governing LiPF6-induced toxicity.

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