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Myeloid‐derived suppressor cell (MDSC)‐like adherent cells (MLACs) are a recently identified CD11b+F4/80− myeloid cell subset that can infiltrate tumors early in development and promote their growth. Because of these functions, MLACs play an important role in establishing an immunosuppressive tumor microenvironment (TME). However, the lack of MLAC‐specific markers has hampered further characterization of this cell type. This study identifies the gene signature of MLACs by analyzing RNA‐sequencing (RNA‐seq) and public single‐cell RNA‐seq data, revealing that MLACs are an independent cell population that are distinct from other intratumoral myeloid cells. After combining proteome analysis of membrane proteins with RNA‐seq data, H2‐Ab1 and CD11c are indicated as marker proteins that can support the isolation of MLAC subsets from CD11b+F4/80− myeloid cells by fluorescence‐activated cell sorting. The CD11b+F4/80−H2‐Ab1+ and CD11b+F4/80−CD11c+ MLAC subsets represent approximately half of the MLAC population that is isolated based on their adhesion properties and possess gene signatures and functional properties similar to those of the MLAC population. Additionally, membrane proteome analysis suggests that MLACs express highly heterogeneous surface proteins. This study facilitates an integrated understanding of heterogeneous intratumoral myeloid cells, as well as the molecular and cellular details of the development of an immunosuppressive TME. [ABSTRACT FROM AUTHOR]

Protein clustering is a ubiquitous event in diverse cellular processes. Self‐association of proteins triggers recruitment of downstream proteins to regulate cellular signaling. To investigate the interactions in detail, chemical biology tools to identify proteins recruited to defined assemblies are required. Here, we exploit an identification of proteins recruited in artificial granules (IPRAG) platform that combines intracellular Y15‐based supramolecule construction with a proximity labeling method. We validated the IPRAG tool using Nck1 as a target bait protein. We constructed Nck1‐tethering granules, labeled the recruited proteins with biotin, and analyzed them by LC‐MS/MS. As a result, we successfully identified proteins that directly or indirectly interact with Nck1. [ABSTRACT FROM AUTHOR]

Escherichia coli has multiple pathways to release nonproductive ribosome complexes stalled at the 3′ end of nonstop mRNA: tmRNA (SsrA RNA)‐mediated trans‐translation and stop codon‐independent termination by ArfA/RF2 or ArfB (YaeJ). The arfA mRNA lacks a stop codon and its expression is repressed by trans‐translation. Therefore, ArfA is considered to complement the ribosome rescue activity of trans‐translation, but the physiological situations in which ArfA is expressed have not been elucidated. Here, we found that the excision of CP4‐57 prophage adjacent to E. coli ssrA leads to the inactivation of tmRNA and switches the primary rescue pathway from trans‐translation to ArfA/RF2. This "rescue‐switching" rearranges not only the proteome landscape in E. coli but also the phenotype such as motility. Furthermore, among the proteins with significantly increased abundance in the ArfA+ cells, we found ZntR, whose mRNA is transcribed together as the upstream part of nonstop arfA mRNA. Repression of ZntR and reconstituted model genes depends on the translation of the downstream nonstop ORFs that trigger the trans‐translation‐coupled exonucleolytic degradation by polynucleotide phosphorylase (PNPase). Namely, our studies provide a novel example of trans‐translation‐dependent regulation and re‐define the physiological roles of prophage excision. [ABSTRACT FROM AUTHOR]