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Review
. 2024 May 8;108(1):328.
doi: 10.1007/s00253-023-12971-w.

Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance

Yi Yang  1   2   3 , Pengzhi Wang  1   2   3 , Samir El Qaidi  4 , Philip R Hardwidge  4 , Jinlin Huang  5   6   7 , Guoqiang Zhu  8   9   10
Affiliations
Review

Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance

Yi Yang et al. Appl Microbiol Biotechnol. .

Abstract

Pseudogenes are defined as "non-functional" copies of corresponding parent genes. The cognition of pseudogenes continues to be refreshed through accumulating and updating research findings. Previous studies have predominantly focused on mammals, but pseudogenes have received relatively less attention in the field of microbiology. Given the increasing recognition on the importance of pseudogenes, in this review, we focus on several aspects of microorganism pseudogenes, including their classification and characteristics, their generation and fate, their identification, their abundance and distribution, their impact on virulence, their ability to recombine with functional genes, the extent to which some pseudogenes are transcribed and translated, and the relationship between pseudogenes and viruses. By summarizing and organizing the latest research progress, this review will provide a comprehensive perspective and improved understanding on pseudogenes in microorganisms. KEY POINTS: • Concept, classification and characteristics, identification and databases, content, and distribution of microbial pseudogenes are presented. • How pseudogenization contribute to pathogen virulence is highlighted. • Pseudogenes with potential functions in microorganisms are discussed.

Keywords: Evolution; Microbiology; Pathogen; Pathogenicity; Pseudogene.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Cartoon illustration of different types of pseudogenes and pseudogenization. A schematic diagram of the A duplicated pseudogene, B retropseudogene pseudogene, and C the CircRNA-derived pseudogene
Fig. 2
Fig. 2
Implication of pseudogenes in oxidative stress response, bacterial infection, and evasion of host immune response in Salmonella. The examples include elucidating the mechanisms by which pseudogenization enhances virulence in Salmonella
Fig. 3
Fig. 3
How pseudogenization of fepE optimizes capsule-mediated respiratory burst evasion by S. Typhi. A Structural schematic of LPS. B Three types of LPS according to the number of O-antigen repeat units. C Pseudogenization of fepE gene is responsible for the lack of LPS that with VL O-antigen chain in S. Typhi. D A diagram showing the brief composition and structure of S. Typhi. E A local magnification of the circular area in Fig. 3D. The capsule shields underlying surface structures from IgM recognition. Repair of ψfepE results in the production of LPS with VL O-antigen chain, which is exposed outside of the capsule, thereby resulting in IgM binding
Fig. 4
Fig. 4
Pseudogenization of rfbE gene mediated respiratory burst evasion by S. Paratyphi A. A Gene clusters responsible for O-antigen biosynthesis in the indicated Salmonella serovars. B Pseudogenization of rfbE gene results in the production of O2 antigen in S. Paratyphi A. C A diagram showing the brief composition and structure of S. Paratyphi A. D A local magnification of the circular area in C. The VL LPS of S. Paratyphi A contains the O2 antigen which is not recognized by IgM. Mutants containing the O9 antigen (ψrfbE repaired) or the O4 antigen can be recognized by IgM
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