Computational analysis of LexA regulons in Proteus species

Mandelonitrile produced by commensal bacteria protects the Colorado potato beetle against predation

Larvae and adults of the Colorado potato beetle (Leptinotarsa decemlineata), a major pest of potato crops, display conspicuous coloration to advertise their toxicity to predators. However, the identity of the toxic compounds remains unclear. Here, we show that larvae and adults release toxic hydrogen cyanide (HCN) from the degradation of mandelonitrile and other cyano-compounds, which are produced by commensal bacteria. We isolate the bacterium Proteus vulgaris Ld01 from the insect's gut, and show that it produces HCN and a mandelonitrile-producing cyanoglucoside, amygdalin. Knockout of a gene (hcnB) encoding putative hydrogen cyanide synthase impairs HCN production in P. vulgaris Ld01. Antibiotic treatment of larvae, to eliminate their commensal bacteria, leads to a substantial reduction of HCN emission in larvae and adults. HCN release by bacteria-deprived beetles can be restored by addition of mandelonitrile or by re-infection with P. vulgaris Ld01 (but not with its ∆hcnB1 or ∆hcnB2 mutants). Finally, we use dual-choice experiments to show that domestic chicks prefer to eat bacteria-deprived larvae over control larvae, larvae re-colonized with P. vulgaris Ld01, or mandelonitrile-injected larvae. Our work highlights the role of the beetle's intestinal bacteria in the production of the cyanoglucoside amygdalin and its derived metabolites, including mandelonitrile and HCN, which protect the insect from predation.

Identification of iron-responsive genes in Proteus vulgaris

Iron is essential for almost all bacteria, and iron homeostasis is precisely controlled by the ferric uptake regulator (Fur). The Fur regulons have been well characterized in some model bacteria, yet little is known in the common opportunistic pathogen Proteus vulgaris. In this study, Fur regulon and iron-responsive genes in P. vulgaris were mainly defined by in silico and proteomic analyses. The results showed that about 250 potential Fur-regulated operons including 14 transcriptional factors were predicted, while 559 proteins exhibited differential expression in response to iron deficiency, not all being directly regulated by Fur, such as transcriptional factors lexA, recA, narL, and arcA. Collectively, these results demonstrated that Fur functioned as a global regulatory protein to repress or activate expression of a large repertoire of genes in P. vulgaris; besides, not all the iron-responsive genes were directly regulated by Fur, whereas indirectly regulated through other mechanisms such as additional transcriptional regulatory proteins.

Identification of the key functional genes in salt-stress tolerance of Cyanobacterium Phormidium tenue using in silico analysis

The development of artificial biocrust using cyanobacterium Phormidium tenue has been suggested as an effective strategy to prevent soil degradation. Here, a combination of in silico approaches with growth rate, photosynthetic pigment, morphology, and transcript analysis was used to identify specific genes and their protein products in response to 500 mM NaCl in P. tenue. The results show that 500 mM NaCl induces the expression of genes encoding glycerol-3-phosphate dehydrogenase (glpD) as a Flavoprotein, ribosomal protein S12 methylthiotransferase (rimO), and a hypothetical protein (sll0939). The constructed co-expression network revealed a group of abiotic stress-responsive genes. Using the Basic Local Alignment Search Tool (BLAST), the homologous proteins of rimO, glpD, and sll0939 were identified in the P. tenue genome. Encoded proteins of glpD, rimO, and DUF1622 genes, respectively, contain (DAO and DAO C), (UPF0004, Radical SAM and TRAM 2), and (DUF1622) domains. The predicted ligand included 22B and MG for DUF1622, FS5 for rimO, and FAD for glpD protein. There was no direct disruption in ligand-binding sites of these proteins by Na+, Cl-, or NaCl. The growth rate, photosynthetic pigment, and morphology of P. tenue were investigated, and the result showed an acceptable tolerance rate of this microorganism under salt stress. The quantitative real-time polymerase chain reaction (qRT-PCR) results revealed the up-regulation of glpD, rimO, and DUF1622 genes under salt stress. This is the first report on computational and experimental analyses of the glpD, rimO, and DUF1622 genes in P. tenue under salt stress to the best of our knowledge.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03050-w.