scholarly journals Molecular Mimicry of Pathogenicity of Neisseria

2021 ◽  
Author(s):  
Indrani Sarkar ◽  
Prateek Dey ◽  
Saurabh Singh Rathore ◽  
Gyan Dev Singh ◽  
Ram Pratap Singh
Keyword(s):  
Comparative Genomics ◽  
Bacterial Resistance ◽  
Antimicrobial Agents ◽  
Molecular Mimicry ◽  
Synonymous Codon ◽  
Clinical Importance ◽  
Synonymous Codon Usage ◽  
Human Interaction ◽  
Evolutionary Analysis ◽  
Long Run

Abstract Neisseria, a genus from beta-proteobacteria class, is of potent clinical importance. This genus contains both pathogenic and commensal strains. Gonorrhea and meningitis are two major diseases caused by pathogens belonging to this genus. With increased use of antimicrobial agents against these pathogens they have evolved the antimicrobial resistance (AMR) capacity making these diseases nearly untreatable. The set of anti-bacterial resistance genes (resistome) and genes associated with signal processing (secretomes) are crucial for the host-microbial interaction. With the virtue of whole genome sequences and computational biology it is now possible to study the genomic and proteomic riddles of Neisseria along with their comprehensive evolutionary and metabolic profiling. We have studied relative synonymous codon usage, amino acid usage, reverse ecology, comparative genomics, evolutionary analysis and pathogen-host (Neisseria-human) interaction through bioinformatics analysis. Our analysis revealed the co-evolution of Neisseria genomes with the human host. Moreover, co-occurrence of Neisseria and humans has been supported through reverse ecology analysis. A differential pattern of evolutionary rate of resistomes and secretomes was evident among the pathogenic and commensal strains. Comparative genomics supported the presence of virulent genes in both pathogenic and commensal strains of select genus. Our analysis also indicated a transition from commensal to pathogenic Neisseria strains through the long run of evolution.

scholarly journals Economic Impacts of Banning Subtherapeutic Use of Antibiotics in Swine Production

2002 ◽  
Vol 34 (3) ◽  
pp. 489-500 ◽  
Author(s):  
B. Wade Brorsen ◽  
Terry Lehenbauer ◽  
Dasheng Ji ◽  
Joe Connor
Keyword(s):  
Public Health ◽  
Bacterial Resistance ◽  
Antimicrobial Agents ◽  
Economic Effects ◽  
Swine Production ◽  
Livestock Feed ◽  
Long Run ◽  
Short Run ◽  
Public Health Officials ◽  
Growth Promotants

Public health officials and physicians are concerned about possible development of bacterial resistance and potential effects on human health that may be related to the use of antimicrobial agents in livestock feed. The focus of this research is aimed at determining the economic effects that subtherapeutic bans of antimicrobials would have on both swine producers and consumers. The results show that a ban on growth promotants for swine would be costly, totaling $242.5 million annually, with swine producers sharing the larger portion in the short run and consumers sharing the larger portion in the long run.

scholarly journals Evolution of codon usage in 2019-new coronavirus causing human infection

2020 ◽  
Author(s):  
Xiaoting Yao ◽  
Yanfei Xie ◽  
Xiong Guan ◽  
Silu Ni ◽  
Chenxiang Zuo ◽  
...  
Keyword(s):  
Codon Usage ◽  
Synonymous Codon ◽  
Viral Evolution ◽  
Synonymous Codon Usage ◽  
Human Infection ◽  
Evolutionary Analysis ◽  
Global Public Health ◽  
Recent Emergence ◽  
Usage Patterns ◽  
Novel Coronavirus

Abstract Background: The recent emergence of viral pneumonia was caused by the novel coronavirus (SARS-Cov-2), which has spread to many countries and threated the global public health.Results: In the current study, we provide a primary evolutionary analysis based on the codon usage patterns of SARS-Cov-2 genome sequences. We employed bioinformatics technologies to measure the nucleotide compositions, the relative synonymous codon usage (RSCU), the codon adaptation index (CAI), and other indices. Our results reflected that there were some similarities of codon usage bias between SARS-Cov-2 and its natural reservoirs, suggesting that SARS-Cov-2 was tended to evolve its codon usage which was comparable to that of its hosts. Additionally, various degree of adaptation to the SARS-Cov-2 host and vector were estimated, even different genes have different codon adaptation to their reservoirs. We further suggested that SARS-Cov-2 isolates were evolving at a rapid substitution rate under their translation selection pressure of their hosts.Conclusions: The findings of the present study will provide help for the understanding of the elements leading to viral evolution and adaptation to reservoirs.

Codon Usage Bias Covaries With Expression Breadth and the Rate of Synonymous Evolution in Humans, but This Is Not Evidence for Selection

Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 1191-1199
Author(s):  
Araxi O Urrutia ◽  
Laurence D Hurst
Keyword(s):  
Codon Usage ◽  
Codon Bias ◽  
Synonymous Codon ◽  
Nucleotide Composition ◽  
Synonymous Codon Usage ◽  
Synonymous Substitutions ◽  
Numerous Species ◽  
Nucleotide Content ◽  
Expression Breadth ◽  
Human Genes

Abstract In numerous species, from bacteria to Drosophila, evidence suggests that selection acts even on synonymous codon usage: codon bias is greater in more abundantly expressed genes, the rate of synonymous evolution is lower in genes with greater codon bias, and there is consistency between genes in the same species in which codons are preferred. In contrast, in mammals, while nonequal use of alternative codons is observed, the bias is attributed to the background variance in nucleotide concentrations, reflected in the similar nucleotide composition of flanking noncoding and exonic third sites. However, a systematic examination of the covariants of codon usage controlling for background nucleotide content has yet to be performed. Here we present a new method to measure codon bias that corrects for background nucleotide content and apply this to 2396 human genes. Nearly all (99%) exhibit a higher amount of codon bias than expected by chance. The patterns associated with selectively driven codon bias are weakly recovered: Broadly expressed genes have a higher level of bias than do tissue-specific genes, the bias is higher for genes with lower rates of synonymous substitutions, and certain codons are repeatedly preferred. However, while these patterns are suggestive, the first two patterns appear to be methodological artifacts. The last pattern reflects in part biases in usage of nucleotide pairs. We conclude that we find no evidence for selection on codon usage in humans.

scholarly journals Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Giovanni Franzo ◽  
Claudia Maria Tucciarone ◽  
Matteo Legnardi ◽  
Mattia Cecchinato
Keyword(s):  
Codon Usage ◽  
Codon Bias ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Accessory Proteins ◽  
Effective Number ◽  
Genome Composition ◽  
Infectious Bronchitis ◽  
Selective Forces ◽  
Effective Number Of Codons

Abstract Background Infectious bronchitis virus (IBV) is one of the most relevant viruses affecting the poultry industry, and several studies have investigated the factors involved in its biological cycle and evolution. However, very few of those studies focused on the effect of genome composition and the codon bias of different IBV proteins, despite the remarkable increase in available complete genomes. In the present study, all IBV complete genomes were downloaded (n = 383), and several statistics representative of genome composition and codon bias were calculated for each protein-coding sequence, including but not limited to, the nucleotide odds ratio, relative synonymous codon usage and effective number of codons. Additionally, viral codon usage was compared to host codon usage based on a collection of highly expressed genes in IBV target and nontarget tissues. Results The results obtained demonstrated a significant difference among structural, non-structural and accessory proteins, especially regarding dinucleotide composition, which appears under strong selective forces. In particular, some dinucleotide pairs, such as CpG, a probable target of the host innate immune response, are underrepresented in genes coding for pp1a, pp1ab, S and N. Although genome composition and dinucleotide bias appear to affect codon usage, additional selective forces may act directly on codon bias. Variability in relative synonymous codon usage and effective number of codons was found for different proteins, with structural proteins and polyproteins being more adapted to the codon bias of host target tissues. In contrast, accessory proteins had a more biased codon usage (i.e., lower number of preferred codons), which might contribute to the regulation of their expression level and timing throughout the cell cycle. Conclusions The present study confirms the existence of selective forces acting directly on the genome and not only indirectly through phenotype selection. This evidence might help understanding IBV biology and in developing attenuated strains without affecting the protein phenotype and therefore immunogenicity.

scholarly journals The Lactococcal dgkB (yecE) and dxsA Genes for Lipid Metabolism Are Involved in the Resistance to Cell Envelope-Acting Antimicrobials

2021 ◽  
Vol 22 (3) ◽  
pp. 1014
Author(s):  
Aleksandra Tymoszewska ◽  
Tamara Aleksandrzak-Piekarczyk
Keyword(s):  
Antimicrobial Peptides ◽  
Bacterial Resistance ◽  
Antimicrobial Agents ◽  
Cytoplasmic Membrane ◽  
Cross Resistance ◽  
Resistant Bacteria ◽  
Membrane Targeting ◽  
Nucleotide Polymorphisms ◽  
Next Generation ◽  
Lipid Ii

The emergence of antibiotic-resistant bacteria led to an urgent need for next-generation antimicrobial agents with novel mechanisms of action. The use of positively charged antimicrobial peptides that target cytoplasmic membrane is an especially promising strategy since essential functions and the conserved structure of the membrane hinder the development of bacterial resistance. Aureocin A53- and enterocin L50-like bacteriocins are highly cationic, membrane-targeting antimicrobial peptides that have potential as next-generation antibiotics. However, the mechanisms of resistance to these bacteriocins and cross-resistance against antibiotics must be examined before application to ensure their safe use. Here, in the model bacterium Lactococcus lactis, we studied the development of resistance to selected aureocin A53- and enterocin L50-like bacteriocins and its correlation with antibiotics. First, to generate spontaneous resistant mutants, L.lactis was exposed to bacteriocin BHT-B. Sequencing of their genomes revealed single nucleotide polymorphisms (SNPs) in the dgkB (yecE) and dxsA genes encoding diacylglycerol kinase and 1-deoxy-D-xylulose 5-phosphate synthase, respectively. Then, selected mutants underwent susceptibility tests with a wide array of bacteriocins and antibiotics. The highest alterations in the sensitivity of studied mutants were seen in the presence of cytoplasmic membrane targeting bacteriocins (K411, Ent7, EntL50, WelM, SalC, nisin) and antibiotics (daptomycin and gramicidin) as well as lipid II cycle-blocking bacteriocins (nisin and Lcn972) and antibiotics (bacitracin). Interestingly, decreased via the SNPs accumulation sensitivity to membrane-active bacteriocins and antibiotics resulted in the concurrently increased vulnerability to bacitracin, carbenicillin, or chlortetracycline. It is suspected that SNPs may result in alterations to the efficiency of the nascent enzymes rather than a total loss of their function as neither deletion nor overexpression of dxsA restored the phenotype observed in spontaneous mutants.

scholarly journals The Effect of Multiple Evolutionary Selections on Synonymous Codon Usage of Genes in the Mycoplasma bovis Genome

PLoS ONE ◽  
2014 ◽  
Vol 9 (10) ◽  
pp. e108949 ◽  
Author(s):  
Jian-hua Zhou ◽  
Yao-zhong Ding ◽  
Ying He ◽  
Yue-feng Chu ◽  
Ping Zhao ◽  
...  
Keyword(s):  
Codon Usage ◽  
Synonymous Codon ◽  
Synonymous Codon Usage ◽  
Mycoplasma Bovis
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