Biology subjects

He, B.-B.

Publications and source records attributed to He, B.-B..

3 recordsLinked to original sources

bioRxiv2023

Combinatorial in silico approach for cancer-associated 4Fe-4S protein discovery

Iron-sulfur (Fe-S) proteins play vital roles in multiple cellular processes, including mediating redox balance as well as DNA replication and repair. Given the role of Fe-S cofactors in genome maintenance, mutations in such metalloproteins could be associated with cancer. Nevertheless, only a few cancer-associated Fe-S proteins have been identified. In vitro, Fe-S cluster is susceptible to degradation in oxic environment. It could also be replaced by other metal ions during protein purification, mis-labelled as zinc finger or Zn-containing proteins. In silico, bioinorganic Fe-S cluster lacks unique sequence characteristics that distinguish itself from other metal-coordination sites, making motif prediction based solely on protein sequence difficult. Thus, in this study, three traits have been employed to discover putative cancer-associated 4Fe-4S proteins. Here, we have analyzed the human proteome via a three-pronged approach: (i) the presence of a triamino acid motif, (ii) the geometric arrangements of the cysteines, and (iii) the mutations of cancer-associated cysteines. In addition to MUTYH, a known 4Fe-4S human DNA glycosylase, 21 novel proteins were discovered as potential cancer-associated 4Fe-4S proteins. While 6 receptor proteins and 3 growth factors have been identified as potential targets in this study, 5 histone lysine methyltransferases with SET domains were also predicted to contain 4Fe-4S metallocofactors. This work provides insights for rational adjustments in experimental design and novel cancer biomarker discovery.

bioinformatics↗

bioRxiv2023

Biosynthesis- and Metabolomics-guided discovery of antimicrobial cyclopeptides against drug-resistant clinical isolates

Antimicrobial resistance remains a significant global threat, contributing significantly to mortality rates worldwide. Ribosomally synthesized and post-translationally modified peptides (RiPPs) have emerged as a promising source of novel peptide antibiotics due to their diverse chemical structures. Here, we reported the discovery of new Avi(Me)Cys-containing cyclopeptide antibiotics through a synergistic approach that combines rule-based genome mining, automated metabolomic analysis, and heterologous expression. We first bioinformatically identified 1,172 RiPP biosynthetic gene clusters (BGCs) responsible for Avi(Me)Cys-containing cyclopeptides from a vast pool of over 50,000 bacterial genomes. Subsequently, we successfully established the connection between three newly identified BGCs and the synthesis of five new peptide antibiotics. Notably, massatide A displayed excellent activity against a spectrum of gram-positive pathogens, including drug-resistant clinical isolates like linezolid-resistant S. aureus and methicillin-resistant S. aureus, with a minimum inhibitory concentration (MIC) of 0.25 g/mL. The remarkable performance of massatide A in an animal infection model, coupled with a low risk of resistance and favorable safety profile, positions it as a promising candidate for antibiotic development. Our study highlights the potential of Avi(Me)Cys-containing cyclopeptides in expanding the arsenal of antibiotics against multi-drug-resistant bacteria, offering promising drug leads in the ongoing battle against infectious diseases.

biochemistry↗

bioRxiv2023

Bacterial Cytochrome P450-catalyzed Post-translational Macrocyclization

Bacterial cytochrome P450s represent an emerging enzyme family that can modify ribosomally synthesized peptides to generate structurally complex macrocyclic skeletons. However, the functional sequence space of this type of enzyme is largely unexplored. In this study, we conduct a systematic genome mining of small ribosomal peptide-tailoring P450s from genomes of actinobacteria via a precursor-centric, primary sequence-, and structure-guided strategy. We uncovered 1,957 putative P450s, prioritized two representative families for functional study, and characterized two P450 enzymes that can respectively catalyze Tyrosine-to-Tryptophan and Tryptophan-to-Tryptophan crosslinks to form 3-mer or 4-mer macrocycle. These two P450 enzymes exhibit broad substrate selectivity, suggesting a promising starting template for engineering unnatural cyclic peptide construction. Our work expanded the enzymatic catalysis of P450s and could inspire the community to discover hidden peptide-modifying enzymes.

biochemistry↗