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Computational analysis of LexA regulons in Proteus species.

ABSTRACT: To gain a general understanding of the SOS system in Proteus species, in this study LexA-binding sites and the LexA regulons in 23 Proteus genomes were first predicted by phylogenetic footprinting server, then with Proteus vulgaris as an example, the expression of LexA regulon in iron limitation was investigated by proteomic analysis and quantitative reverse transcription polymerase chain reaction (RT-qPCR) method. The results showed that LexA proteins were highly conserved in Proteus species, and were in a close phylogenetic relationship with those in Gram-negative bacteria; the core SOS response genes lexA and recA were found in all the 23 genomes, indicating that this system was widely distributed in this genus; besides that, putative LexA-binding sites were also found in the upstream sequences of some genes involved in other biological processes such as biosynthesis, drug resistance, and stress response. Proteomic and RT-qPCR analyses showed that under iron deficient condition, the expression of lexA, recA and sulA was transcriptionally upregulated (p < 0.05), lexA was also translationally upregulated but recA was on the contrary (p < 0.05), whereas another SOS response gene dinI was transcriptionally downregulated (p < 0.01). These results indicated that in response to iron deficiency, the members of LexA regulon were not regulated by the same way, suggesting the existence of a precise regulation mechanism of SOS response in P. vulgaris. In conclusion, this study provided a preliminary understanding of the SOS system in Proteus species, which laid the foundation for further investigation of its roles in SOS response and other biological processes.

SUBMITTER: Lu Y

PROVIDER: S-EPMC7895892 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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Computational analysis of LexA regulons in Proteus species.

Lu Yongzhong Y Cheng Linyue L

3 Biotech 20210219 3

To gain a general understanding of the SOS system in Proteus species, in this study LexA-binding sites and the LexA regulons in 23 Proteus genomes were first predicted by phylogenetic footprinting server, then with Proteus vulgaris as an example, the expression of LexA regulon in iron limitation was investigated by proteomic analysis and quantitative reverse transcription polymerase chain reaction (RT-qPCR) method. The results showed that LexA proteins were highly conserved ...[more]

PMID: 33680696

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Project description:BackgroundThe transcription factor LexA plays an important role in the SOS response in Escherichia coli and many other bacterial species studied. Although the lexA gene is encoded in almost every bacterial group with a wide range of evolutionary distances, its precise functions in each group/species are largely unknown. More recently, it has been shown that lexA genes in two cyanobacterial genomes Nostoc sp. PCC 7120 and Synechocystis sp. PCC 6803 might have distinct functions other than the regulation of the SOS response. To gain a general understanding of the functions of LexA and its evolution in cyanobacteria, we conducted the current study.ResultsOur analysis indicates that six of 33 sequenced cyanobacterial genomes do not harbor a lexA gene although they all encode the key SOS response genes, suggesting that LexA is not an indispensable transcription factor in these cyanobacteria, and that their SOS responses might be regulated by different mechanisms. Our phylogenetic analysis suggests that lexA was lost during the course of evolution in these six cyanobacterial genomes. For the 26 cyanobacterial genomes that encode a lexA gene, we have predicted their LexA-binding sites and regulons using an efficient binding site/regulon prediction algorithm that we developed previously. Our results show that LexA in most of these 26 genomes might still function as the transcriptional regulator of the SOS response genes as seen in E. coli and other organisms. Interestingly, putative LexA-binding sites were also found in some genomes for some key genes involved in a variety of other biological processes including photosynthesis, drug resistance, etc., suggesting that there is crosstalk between the SOS response and these biological processes. In particular, LexA in both Synechocystis sp. PCC6803 and Gloeobacter violaceus PCC7421 has largely diverged from those in other cyanobacteria in the sequence level. It is likely that LexA is no longer a regulator of the SOS response in Synechocystis sp. PCC6803.ConclusionsIn most cyanobacterial genomes that we analyzed, LexA appears to function as the transcriptional regulator of the key SOS response genes. There are possible couplings between the SOS response and other biological processes. In some cyanobacteria, LexA has adapted distinct functions, and might no longer be a regulator of the SOS response system. In some other cyanobacteria, lexA appears to have been lost during the course of evolution. The loss of lexA in these genomes might lead to the degradation of its binding sites.

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Computational analysis of LexA regulons in Proteus species.

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Computational analysis of LexA regulons in <i>Proteus</i> species.

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