PREDICTING ANTISENSE RNAs IN THE GENOMES OF ESCHERICHIA COLI AND SALMONELLA TYPHIMURIUM USING PROMOTER-SEARCH ALGORITHM PLATPROM

2006 ◽  
Vol 04 (02) ◽  
pp. 443-454 ◽  
Author(s):  
OLGA N. OZOLINE ◽  
ALEXANDER A. DEEV
Keyword(s):  
Escherichia Coli ◽  
Salmonella Typhimurium ◽  
Search Algorithm ◽  
Bacterial Species ◽  
Coding Sequences ◽  
Template Strand ◽  
Homologous Genes ◽  
Intergenic Regions ◽  
Recognition Software ◽  
Very High

A pattern recognition software PlatProm, which takes into consideration both sequence-specific and structure-specific features in the genetic environment of the promoter sites and identifies transcription start points with a very high accuracy was used to reveal potentially transcribed regions in the genomes of two bacterial species. Along with the expected promoters located upstream from coding sequences PlatProm identified several hundred of very similar signals in other intergenic regions and within coding sequences. Homologous genes of Escherichia coli and Salmonella typhimurium, containing potential promoters on the template strand are suggested as putative targets for regulations by antisense RNA-products (aRNAs).

scholarly journals Deletion Formation Between the Two Salmonella typhimurium Flagellin Genes Encoded on the Mini F Plasmid: Escherichia coli ssb Alleles Enhance Deletion Rates and Change Hot-Spot Preference for Deletion Endpoints

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 563-572 ◽  
Author(s):  
Takafumi Mukaihara ◽  
Masatoshi Enomoto
Keyword(s):  
Escherichia Coli ◽  
Salmonella Typhimurium ◽  
Hot Spots ◽  
Hot Spot ◽  
Direct Repeats ◽  
Replication Slippage ◽  
Detection Systems ◽  
Deletion Formation ◽  
Homologous Sequences ◽  
Deletion Detection

Deletion formation between the 5′-mostly homologous sequences and between the 3′-homeologous sequences of the two Salmonella typhimurium flagellin genes was examined using plasmid-based deletion-detection systems in various Escherichia coli genetic backgrounds. Deletions in plasmid pLC103 occur between the 5′ sequences, but not between the 3′ sequences, in both RecA-independent and RecA-dependent ways. Because the former is predominant, deletion formation in a recA background depends on the length of homologous sequences between the two genes. Deletion rates were enhanced 30- to 50-fold by the mismatch repair defects, mutS, mutL and uvrD, and 250-fold by the ssb-3 allele, but the effect of the mismatch defects was canceled by the ΔrecA allele. Rates of the deletion between the 3′ sequences in plasmid pLC107 were enhanced 17- to 130-fold by ssb alleles, but not by other alleles. For deletions in pLC107, 96% of the endpoints in the recA+ background and 88% in ΔrecA were in the two hot spots of the 60- and 33-nucleotide (nt) homologous sequences, whereas in the ssb-3 background >50% of the endpoints were in four- to 14-nt direct repeats dispersed in the entire 3′ sequences. The deletion formation between the homeologous sequences is RecA-independent but depends on the length of consecutive homologies. The mutant ssb allele lowers this dependency and results in the increase in deletion rates. Roles of mutant SSB are discussed with relation to misalignment in replication slippage.

scholarly journals Autophagy—A Story of Bacteria Interfering with the Host Cell Degradation Machinery

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 110
Author(s):  
Anna K. Riebisch ◽  
Sabrina Mühlen ◽  
Yan Yan Beer ◽  
Ingo Schmitz
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Immune Response ◽  
Mycobacterium Tuberculosis ◽  
Listeria Monocytogenes ◽  
Salmonella Typhimurium ◽  
Innate Immune ◽  
Intracellular Pathogens ◽  
Response Mechanism ◽  
Pathogenic Escherichia Coli

Autophagy is a highly conserved and fundamental cellular process to maintain cellular homeostasis through recycling of defective organelles or proteins. In a response to intracellular pathogens, autophagy further acts as an innate immune response mechanism to eliminate pathogens. This review will discuss recent findings on autophagy as a reaction to intracellular pathogens, such as Salmonella typhimurium, Listeria monocytogenes, Mycobacterium tuberculosis, Staphylococcus aureus, and pathogenic Escherichia coli. Interestingly, while some of these bacteria have developed methods to use autophagy for their own benefit within the cell, others have developed fascinating mechanisms to evade recognition, to subvert the autophagic pathway, or to escape from autophagy.

How Optimized Is the Translational Machinery in Escherichia coli, Salmonella typhimurium and Saccharomyces cerevisiae?

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 37-44 ◽  
Author(s):  
Xuhua Xia
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Salmonella Typhimurium ◽  
Codon Usage ◽  
Translational Efficiency ◽  
Square Root ◽  
Translational Machinery ◽  
Mutual Adaptation ◽  
Trna Species

Abstract The optimization of the translational machinery in cells requires the mutual adaptation of codon usage and tRNA concentration, and the adaptation of tRNA concentration to amino acid usage. Two predictions were derived based on a simple deterministic model of translation which assumes that elongation of the peptide chain is rate-limiting. The highest translational efficiency is achieved when the codon recognized by the most abundant tRNA reaches the maximum frequency. For each codon family, the tRNA concentration is optimally adapted to codon usage when the concentration of different tRNA species matches the square-root of the frequency of their corresponding synonymous codons. When tRNA concentration and codon usage are well adapted to each other, the optimal content of all tRNA species carrying the same amino acid should match the square-root of the frequency of the amino acid. These predictions are examined against empirical data from Escherichia coli, Salmonella typhimurium, and Saccharomyces cerevisiae.

scholarly journals An Understanding of the Global Status of Major Bacterial Pathogens of Milk Concerning Bovine Mastitis: A Systematic Review and Meta-Analysis (Scientometrics)

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 545
Author(s):  
Paramanandham Krishnamoorthy ◽  
Kuralayanapalya P. Suresh ◽  
Kavitha S. Jayamma ◽  
Bibek R. Shome ◽  
Sharanagouda S. Patil ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Management Practices ◽  
Meta Analysis ◽  
Bacterial Species ◽  
Clinical Mastitis ◽  
Therapeutic Interventions ◽  
Coagulase Negative Staphylococcus ◽  
Prevalence Studies ◽  
The World ◽  
Pathogen Prevalence

In this study, the major mastitis pathogen prevalence in the cattle and buffalo of the world was estimated by a meta-analysis. Staphylococcus (S) species, Streptococcus (St) species, and Escherichia coli (Ec) prevalence studies reported during 1979–2019 were collected using online databases, and offline resources. A meta-analysis of these data was done with the meta package in R-Software. The Staphylococcus aureus was the major mastitis pathogen, mostly causing subclinical mastitis, Ec causing clinical mastitis and St causing subclinical and clinical mastitis. The pooled prevalence estimates of S, St, and Ec were 28%, 12%, and 11% in the world from 156, 129, and 92 studies, respectively. The S, St, and Ec prevalences were high in Latin America (51%), Oceania (25%), and Oceania (28%), respectively. Higher S, St, and Ec prevalences were observed by molecular methods, signifying high sensitivity and usefulness for future studies. Among bacterial species, S. aureus (25%) followed by coagulase-negative Staphylococcus species (20%), Escherichia coli (11%), St. agalactiae (9%), St. uberis (9%) were the important pathogens present in the milk of the world. We hypothesize that there is a urgent need to reduce mastitis pathogen prevalence by ensuring scientific farm management practices, proper feeding, therapeutic interventions to augment profits in dairying, and improving animal and human health.

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