Diversity, Distribution, and Chromosomal Rearrangements of TRIP1 Repeat Sequences in

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2024 Feb 24

PMID 38397225

Authors

Zhan Li

Xiong Liu

Nianzhi Ning

Tao Li

Hui Wang

Affiliations

Soon will be listed here.

Abstract

The bacterial genome contains numerous repeated sequences that greatly affect its genomic plasticity. The K-12 genome contains three copies of the TRIP1 repeat sequence (TRIP1a, TRIP1b, and TRIP1c). However, the diversity, distribution, and role of the TRIP1 repeat sequence in the genome are still unclear. In this study, after screening 6725 genomes, the TRIP1 repeat was found in the majority of strains (96%: 6454/6725). The copy number and direction of the TRIP1 repeat sequence varied in each genome. Overall, 2449 genomes (36%: 2449/6725) had three copies of TRIP1 (TRIP1a, TRIP1b, and TRIP1c), which is the same as K-12. Five types of TRIP1 repeats, including two new types (TRIP1d and TRIP1e), are identified in genomes, located in 4703, 3529, 5741, 1565, and 232 genomes, respectively. Each type of TRIP1 repeat is localized to a specific locus on the chromosome. TRIP1 repeats can cause intra-chromosomal rearrangements. A total of 156 rearrangement events were identified, of which 88% (137/156) were between TRIP1a and TRIP1c. These findings have important implications for future research on TRIP1 repeats.

References

Smirnov G . [Repeats in bacterial genomes: evolutionary considerations]. Mol Gen Mikrobiol Virusol. 2010; (2):11-20. View

Lu H, Patil P, Van Sluys M, White F, Ryan R, Dow J . Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas. PLoS One. 2008; 3(11):e3828. PMC: 2585010. DOI: 10.1371/journal.pone.0003828. View

Partridge S, Hall R . The IS1111 family members IS4321 and IS5075 have subterminal inverted repeats and target the terminal inverted repeats of Tn21 family transposons. J Bacteriol. 2003; 185(21):6371-84. PMC: 219399. DOI: 10.1128/JB.185.21.6371-6384.2003. View

cutova M, Manta J, Porubiakova O, Kaura P, Stastny J, Jagelska E . Divergent distributions of inverted repeats and G-quadruplex forming sequences in Saccharomyces cerevisiae. Genomics. 2019; 112(2):1897-1901. DOI: 10.1016/j.ygeno.2019.11.002. View

Wen J, Fozo E . sRNA antitoxins: more than one way to repress a toxin. Toxins (Basel). 2014; 6(8):2310-35. PMC: 4147584. DOI: 10.3390/toxins6082310. View

Mahfooz S, Shankar G, Narayan J, Singh P, Akhter Y . Simple sequence repeat insertion induced stability and potential 'gain of function' in the proteins of extremophilic bacteria. Extremophiles. 2022; 26(2):17. DOI: 10.1007/s00792-022-01265-0. View

Treangen T, Abraham A, Touchon M, Rocha E . Genesis, effects and fates of repeats in prokaryotic genomes. FEMS Microbiol Rev. 2009; 33(3):539-71. DOI: 10.1111/j.1574-6976.2009.00169.x. View

Lioy V, Junier I, Boccard F . Multiscale Dynamic Structuring of Bacterial Chromosomes. Annu Rev Microbiol. 2021; 75:541-561. DOI: 10.1146/annurev-micro-033021-113232. View

Raghavan R, Groisman E, Ochman H . Genome-wide detection of novel regulatory RNAs in E. coli. Genome Res. 2011; 21(9):1487-97. PMC: 3166833. DOI: 10.1101/gr.119370.110. View

10.

Raeside C, Gaffe J, Deatherage D, Tenaillon O, Briska A, Ptashkin R . Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli. mBio. 2014; 5(5):e01377-14. PMC: 4173774. DOI: 10.1128/mBio.01377-14. View

11.

Brazda V, Fojta M, Bowater R . Structures and stability of simple DNA repeats from bacteria. Biochem J. 2020; 477(2):325-339. PMC: 7015867. DOI: 10.1042/BCJ20190703. View

12.

LARKIN M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H . Clustal W and Clustal X version 2.0. Bioinformatics. 2007; 23(21):2947-8. DOI: 10.1093/bioinformatics/btm404. View

13.

Bracher S, Schmidt C, Dittmer S, Jung H . Core Transmembrane Domain 6 Plays a Pivotal Role in the Transport Cycle of the Sodium/Proline Symporter PutP. J Biol Chem. 2016; 291(50):26208-26215. PMC: 5207087. DOI: 10.1074/jbc.M116.753103. View

14.

Dubey S, Majumder P, Penmatsa A, Sardesai A . Topological analyses of the L-lysine exporter LysO reveal a critical role for a conserved pair of intramembrane solvent-exposed acidic residues. J Biol Chem. 2021; 297(4):101168. PMC: 8498466. DOI: 10.1016/j.jbc.2021.101168. View

15.

Gonzalez-Torres P, Rodriguez-Mateos F, Anton J, Gabaldon T . Impact of Homologous Recombination on the Evolution of Prokaryotic Core Genomes. mBio. 2019; 10(1). PMC: 6343036. DOI: 10.1128/mBio.02494-18. View

16.

Grosse C, Scherer J, Koch D, Otto M, Taudte N, Grass G . A new ferrous iron-uptake transporter, EfeU (YcdN), from Escherichia coli. Mol Microbiol. 2006; 62(1):120-31. DOI: 10.1111/j.1365-2958.2006.05326.x. View

17.

Shikov A, Savina I, Nizhnikov A, Antonets K . Recombination in Bacterial Genomes: Evolutionary Trends. Toxins (Basel). 2023; 15(9). PMC: 10534446. DOI: 10.3390/toxins15090568. View

18.

Pathania A, Sardesai A . Distinct Paths for Basic Amino Acid Export in Escherichia coli: YbjE (LysO) Mediates Export of L-Lysine. J Bacteriol. 2015; 197(12):2036-47. PMC: 4438211. DOI: 10.1128/JB.02505-14. View

19.

Meydan S, Klepacki D, Karthikeyan S, Margus T, Thomas P, Jones J . Programmed Ribosomal Frameshifting Generates a Copper Transporter and a Copper Chaperone from the Same Gene. Mol Cell. 2017; 65(2):207-219. PMC: 5270581. DOI: 10.1016/j.molcel.2016.12.008. View

20.

van Belkum A . Short sequence repeats in microbial pathogenesis and evolution. Cell Mol Life Sci. 2001; 56(9-10):729-34. PMC: 11146772. DOI: 10.1007/s000180050019. View