Post-translational changes in Phialophora verrucosa via lysine lactylation during prolonged presence in a patient with a CARD9-related immune disorder

Abstract

CARD9-related inherited immune disorders are a major risk factor for chronic disseminated fungal infection. In addition to pathogens of Candida and dermatophytes, the environmental opportunists of the black yeast-like fungi are relatively frequent in this patient cohort. Particularly the genus Phialophora is overrepresented. We investigated two isolates of a strain of P. verrucosa residing in a CARD9 patient, sampled with a period of ten years apart. Genomes, melanization and antifungal susceptibility of progenitor and derived strains were compared, and potential adaptation to the host habitat was investigated with proteomic techniques using post-translational modification as a proxy. Global lactylation analysis was performed using high accuracy nano-LC-MS/MS in combination with enrichment of lactylated peptides from digested cell lysates, and subsequent peptide identification. The genome of the derived isolate had accumulated 6945 SNPs, of which 31 were detected in CDS. A large number of identified proteins were significantly enriched, e.g. in melanin biosynthesis. A total of 636 lactylation sites on 420 lactylated proteins were identified, which contained in 26 types of modification motifs. Lysine lactylation (Kla) was found in 23 constituent proteins of the ribosome, indicating an impact of Kla in protein synthesis. Twelve lactylated proteins participated in pathogenicity. A protein-protein interaction (PPI) network analysis suggested that protein lactylations are widely distributed influencing various biological processes. Our findings reveal widespread roles for lysine lactylation in regulating metabolism and melanin biosynthesis in black fungi. Several large rearrangements and inversions were observed in the genome, but genomic changes could not be linked to adaptation or to known clinically relevant properties of progenitor to derived isolate; in vitro antifungal susceptibility had largely remained unaltered.

Global profiling of lysine lactylation in human lungs

“…A subcellular localization analysis of the 333 lactylated proteins was conducted by using UniProt database notes. As shown in Figure 3A, most of the lactylated proteins in human lungs were distributed in the cytoplasm (29.8%) and nucleus (29.1%), which is the same as the three subcellular localizations with the most lactylated proteins in human gastric cancer cells and other cell types [14–19]. In addition, our analysis revealed that secreted proteins, proteins associated with chromosomes, proteins in the extracellular space and at other locations were lactylated, demonstrating that the lactylation profile of human lungs shows diverse subcellular distributions (Figure 3A).…”

“…However, it is interesting that the proline (P) residue was found to be enriched in the second position upstream of the Kla site in AGS human gastric cancer cells [11], while in our motifs, it was enriched in the third position downstream of the Kla site. We did not find any same enriched residues in the motifs of other species [15–19], which suggested that lactylated proteins exhibit a specific preference for substrates in different human tissue or cell lines, and the differences among species were great.…”

“…Through a pattern analysis of lactylated sites, we found that the Kla sites were more likely to be located in a coil structure ( p ‐value 1.62E‐04), and the exposure of lactylation sites on the protein surface was higher than that of all other lysine residues ( p ‐value 2.348E‐14). With respect to the sequence motif surrounding Kla residues, we found that isoleucine (I), glutamine (E) and proline (P) residues were enriched in three patterns, which suggested that lactylated proteins show a specific preference for substrates in different human tissues and cell lines, and the differences among the species were great [14–19].…”

Metagenomics reveals an abundance of black yeast‐like fungi in the skin microbiome

“…The skin microbiome consists of viruses, and bacterial and eukaryotic communities, most of which are natural colonisers while others are ephemeral opportunists or are pathogens potentially involved in cutaneous infections 48,60 . Due to its high exposure to the surroundings, the microbial community of the skin surface constantly loses and acquires microbes 57 . Among eukaryotes, Malassezia is the most frequent coloniser, 50,51,57,59 while dermatophytes are the most common pathogenic fungi in the skin microbiome 48 .…”

“…48,60 Due to its high exposure to the surroundings, the microbial community of the skin surface constantly loses and acquires microbes. 57 Among eukaryotes, Malassezia is the most frequent coloniser, 50,51,57,59 while dermatophytes are the most common pathogenic fungi in the skin microbiome. 48 However, some groups have remained unexplored by conventional culture-based methods.…”