The present invention provides a vector construct comprising the following components: (i) a sequence encoding a signal peptide which directs proteins into the Tat secretory pathway; and (ii) a sequence encoding a fluorophore fused to a sequence encoding a pVIII phage coat protein. Nucleic acid molecules comprising components (i) and (ii) are also provided, together with phage particles comprising such vectors or nucleic acid molecules and expressing a fluorophore-pVIII fusion protein on the surface. Methods for producing such fluorescent phage particles are also provided.

Provided are nucleic acids that include a promoter, where the promoter is operable in a Bacteroides cell and is operably linked to a heterologous nucleotide sequence of interest. Also provided are nucleic acids that include a promoter (operable in a prokaryotic cell such as a Bacteroides cell) operably linked to a sequence encoding a synthetic ribosomal binding site (RBS). Also provided are fusion proteins (and nucleic acids encoding them) in which a secreted Bacteroides polypeptide is fused to a heterologous polypeptide of interest. Also provided are prokaryotic cells (e.g., E. coli, a Bacteroides cell, and the like) that include one more nucleic acids such as those described above. Also provided are methods of expression in a prokaryotic cell, methods of detectably labeling a Bacteroides cell in an animal's gut, and methods of delivering a protein to an individual's gut.

Some aspects of this disclosure provide methods for phage-assisted continuous evolution (PACE) of proteases. Some aspects of this invention provide methods for evaluating and selecting protease inhibitors based on the likelihood of the emergence of resistant proteases as determined by the protease PACE methods provided herein. Some aspects of this disclosure provide strategies, methods, and reagents for protease PACE, including fusion proteins for translating a desired protease activity into a selective advantage for phage particles encoding a protease exhibiting such an activity and improved mutagenesis-promoting expression constructs. Evolved proteases that recognize target cleavage sites which differ from their canonical cleavage site are also provided herein.

The present invention relates to a chimeric enzyme comprising or consisting of at least one catalytic domain of a capping enzyme and at least one RNA-binding domain of a protein-RNA tethering system as well as its application for the production of an RNA molecule with a 5′-terminal cap.

In alternative embodiments, provided are compositions comprising chemically or structurally modified bacteriophages of the genus Caudovirales having an exterior or outer surface comprising at least one heterologous carbohydrate binding domain (CBD) comprising a lectin or a plurality of additional homologous CBDs, or more CBDs than found on a comparable wild type (WT) bacteriophage.

The present disclosure is directed to lysin-AMP polypeptide constructs, isolated lysin polypeptides, and pharmaceutical compositions comprising the isolated polypeptides and/or lysin-AMP polypeptide constructs. Methods of using the lysin-AMP polypeptide constructs, isolated lysin polypeptides and pharmaceutical compositions are also herein provided. In addition, isolated polynucleotides encoding the lysin-AMP polypeptide constructs and isolated lysin polypeptides are disclosed herein.

The present disclosure provides a chimeric receptor binding protein (RBP) resistant to proteolytic digestion wherein said RBP comprises a portion of a receptor binding protein derived from a bacteriophage fused through a designed linker region consisting of 1 to 70 amino acids, to a portion of a receptor binding protein derived from a different bacteriophage, wherein said linker region is designed to be resistant to proteolytic digestion.

The present invention provides novel engineered polypeptides that support both reverse transcription and DNA amplification in manganese-independent reactions. The present invention also provides methods for amplifying template nucleic acids using such polypeptides. This invention addresses deficiencies in the current state of the art in nucleic acid amplification-based detection of template nucleic acids, especially RNA targets, including deficiencies in detection sensitivity, specificity, enzyme stability, inhibitor tolerance and time to result compared with manganese-dependent thermostable reverse transcriptases and two-enzyme solutions.

A method of engineering bacteriophages comprising isolating a bacteriophage; removing all attachment genes from a genome of said bacteriophage; inserting a first unique open reading frame encoding one or more attachment genes and inserting a second unique open reading frame encoding one or more genes useful for overcoming bacterial defenses; and inserting a non-natural attachment gene into said first open reading frame, wherein said non-natural attachment gene is specific for attaching to a selected bacteria.

Hybrid nanopores, comprising a protein pore supported within a solid-state membrane, which combine the robust nature of solid-state membranes with the easily tunable and precise engineering of protein nanopores. In an embodiment, a lipid-free hybrid nanopore comprises a water soluble and stable, modified portal protein of the Thermus thermophilus bacteriophage G20c, electrokinetically inserted into a larger nanopore in a solid-state membrane. The hybrid pore is stable and easy to fabricate, and exhibits low peripheral leakage, allowing sensing and discrimination among different types of biomolecules.