Genome Wide Search for Biomarkers to Diagnose Yersinia Infections

Kalia, Vipin Chandra; Kumar, Prasun

doi:10.1007/s12088-015-0552-6

Cited by 27 publications

(24 citation statements)

References 41 publications

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“…However, in cases where bacterial genomes contain multiple copies of rrs, such as in Clostridium, Staphylococcus, Streptococcus, Vibrio, and Yersinia species, a high level of heterogeneity is seen. It is difficult to identify these bacterial species on the basis of their rrs gene alone [5][6][7][8][9][10]. The same problem has been faced in the case of Lactobacillus as well.…”

Section: Discussionmentioning

confidence: 99%

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Comparative Genomics Reveals Biomarkers to Identify Lactobacillus Species

Koul

Kalia

2016

Indian J Microbiol

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Bacteria possessing multiple copies of 16S rRNA (rrs) gene demonstrate high intragenomic heterogeneity. It hinders clear distinction at species level and even leads to overestimation of the bacterial diversity. Fifty completely sequenced genomes belonging to 19 species of Lactobacillus species were found to possess 4-9 copies of rrs each. Multiple sequence alignment of 268 rrs genes from all the 19 species could be classified into 20 groups. Lactobacillus sanfranciscensis TMW 1.1304 was the only species where all the 7 copies of rrs were exactly similar and thus formed a distinct group. In order to circumvent the problem of high heterogeneity arising due to multiple copies of rrs, 19 additional genes (732-3645 nucleotides in size) common to Lactobacillus genomes, were selected and digested with 10 Type II restriction endonucleases (RE), under in silico conditions. The following unique gene-RE combinations: recA (1098 nts)-HpyCH4 V, CviAII, BfuCI and RsaI were found to be useful in identifying 29 strains representing 17 species. Digestion patterns of genes-ruvB (1020 nts), dnaA (1368 nts), purA (1290 nts), dnaJ (1140 nts), and gyrB (1944 nts) in combination with REs-AluI, BfuCI, CviAI, Taq1, and Tru9I allowed clear identification of an additional 14 strains belonging to 8 species. Digestion pattern of genes recA, ruvB, dnaA, purA, dnaJ and gyrB can be used as biomarkers for identifying different species of Lactobacillus.

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Section: Discussionmentioning

confidence: 99%

“…Another limitation generally encountered in the usage of rrs is in the case of organisms which harbour it in multiple copies: Clostridium, Yersinia, Vibrio, Staphylococcus, Streptococcus, etc. Here, high intragenomic heterogeneity leads to mis-identification and even overestimation of bacterial populations [5][6][7][8][9][10].…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomics Reveals Biomarkers to Identify Lactobacillus Species

Koul

Kalia

2016

Indian J Microbiol

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“…A total of 10 Type II REs were considered for digestion on the basis of our previous works [18][19][20]. The following REs were used: (1) 4 base cutters AluI (AG'CT), BfaI (C'TA_G), BfuCI (_GATC'), CviAII (C_AT'G), HpyCH4V (TG'CA), RsaI (GT'AC), TaqI (T_CG'A), Tru9I (T_TA'A), and (2) 6 base cutters HaeI (WGG'CCW), Hin1I (GR_CG'YC).…”

Section: Restriction Endonuclease Analysis Of Common Genesmentioning

confidence: 99%

“…net/) was used to get RE digestion patterns of the 27 common gene sequences (Table S2). Data matrices of REs producing 5-15 fragments were taken into consideration for further analysis [18][19][20].…”

Section: Restriction Endonuclease Analysis Of Common Genesmentioning

confidence: 99%

“…These features enable easy identification of organisms up to the species level. However, rrs gene does not prove helpful in the following scenarios: (1) in phylogenetically very closely related strains, which differ in less than 1 % nts along their length, and (2) in strains with multiple copies of this gene in each genome [17][18][19][20]. An obvious solution to circumvent this problem is to use other HKGs [13,21].…”

Section: Introductionmentioning

confidence: 99%

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A Genome-Wide Profiling Strategy as an Aid for Searching Unique Identification Biomarkers for Streptococcus

Kalia

Kumar

et al. 2015

Indian J Microbiol

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The use of rrs (16S rRNA) gene is widely regarded as the ''gold standard'' for identifying bacteria and determining their phylogenetic relationships. Nevertheless, multiple copies of this gene in a genome is likely to give an overestimation of the bacterial diversity. In each of the 50 Streptococcus genomes (16 species, 50 strains), 4-7 copies of rrs are present. The nucleotide sequences of these rrs genes show high similarity within and among genomes, which did not allow unambiguous identification. A genome-wide search revealed the presence of 27 gene sequences common to all the Streptococcus species. Digestion of these 27 gene sequences with 10 type II restriction endonucleases (REs) showed that unique RE digestion in purH gene is sufficient for clear cut identification of 30 genomes belonging to 16 species. Additional gene-RE combinations allowed identification of another 15 strains belonging to S. pneumoniae, S. pyogenes, and S. suis. For the rest 5 strains, a combination of 2 genes was required for identifying them. The proposed strategy is likely to prove helpful in proper detection of pathogens like Streptococcus.

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The immune system of prokaryotes: potential applications and implications for gene editing

Liu,

Wang

et al. 2024

Biotechnology Journal

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Gene therapy has revolutionized the treatment of genetic diseases. Spearheading this revolution are sophisticated genome editing methods such as TALENs, ZFNs, and CRISPR‐Cas, which trace their origins back to prokaryotic immune systems. Prokaryotes have developed various antiviral defense systems to combat viral attacks and the invasion of genetic elements. The comprehension of these defense mechanisms has paved the way for the development of indispensable tools in molecular biology. Among them, restriction endonuclease originates from the innate immune system of bacteria. The CRISPR‐Cas system, a widely applied genome editing technology, is derived from the prokaryotic adaptive immune system. Single‐base editing is a precise editing tool based on CRISPR‐Cas system that involves deamination of target base. It is worth noting that prokaryotes possess deamination enzymes as part of their defense arsenal over foreign genetic material. Furthermore, prokaryotic Argonauts (pAgo) proteins, also function in anti‐phage defense, play an important role in complementing the CRISPR‐Cas system by addressing certain limitations it may have. Recent studies have also shed light on the significance of Retron, a reverse transcription transposon previously showed potential in genome editing, has also come to light in the realm of prokaryotic immunity. These noteworthy findings highlight the importance of studying prokaryotic immune system for advancing genome editing techniques. Here, both the origin of prokaryotic immunity underlying aforementioned genome editing tools, and potential applications of deaminase, pAgo protein and reverse transcriptase in genome editing among prokaryotes were introduced, thus emphasizing the fundamental mechanism and significance of prokaryotic immunity.

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Genome Wide Search for Biomarkers to Diagnose Yersinia Infections

Cited by 27 publications

References 41 publications

Comparative Genomics Reveals Biomarkers to Identify Lactobacillus Species

Comparative Genomics Reveals Biomarkers to Identify Lactobacillus Species

A Genome-Wide Profiling Strategy as an Aid for Searching Unique Identification Biomarkers for Streptococcus

The immune system of prokaryotes: potential applications and implications for gene editing

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