Nomenclature for Mud Insertions

A variety of phage Mu derivatives (Mud phages) have been used as tranposons for formation of operon and protein fusions. Recently it has been possible to substitute one sort of Mu derivative for another by recombination events internal to the Mud phage that do not alter the insertion site or the flanking sequences in the host chromosome. This has given rise to some problems of nomenclature. We propose the following conventions to solve these problems.

1. The allele number of a Mud insertion is not changed when the nuture of the inserted material is altered by recombination with other Mud phages.

For example: If his-9887::Mud1 is isolated and assigned a his allele number, it retains this number when a KanR determinant is placed in the inserted material. Now it becomes his-9897::MudK (see below for naming of MudK).

2. Since a variety of Mud phages are available and these names fit no apparent uniform system, we propose that a shorthand name be assigned to each phage and be used in naming mutations. Below is a list that includes the Mud derivatives currently in use in our lab.

Shorthand Old Name Ref. Definition
Mud1 MudI (AmpR,Lac) [3] Original operon fusion phage of Casadaban
Mud2 MudII (AmpR,Lac) [2] Protein fusion phage of Casadaban
MudA Mud1-8 [6] Hughes derivative of Mud1 with suppressable transposition defects (operon fusion)
MudB Mud2-8 [6] Hughes derivative of Mud2 with suppressable transposition defects (protein fusions)
MudC MudII4042 [5] Automatic cloning Mud with DNA replication origin (protein fusions)
MudD mini-Mud [4] Intact lac operon including I, Z, Y, and A (no fusions)
MudE mini-Mud [4] Intact lac operon including I, Z, Y, and A in orientation opposite to that in MudD (no fusions)
MudF mini-Mud A KanR derivative of MudD. Still lac+ but carries KanR and a deletion of transposition functions derived from MudK (no fusions)
MudJ MudI1734 [1] A short Mud derivative carrying KanR and a deletion of transposition functions (forms operon fusions)

3. If simple mutations are added to these phages, the genotype can be added to the insertion designation.

For example: A Tn5 insertion in AmpR is available and can be added to any of the Mud phages carrying AmpR. If his-9897::Mud1 receives this Tn5 in AmpR it would be called his-9897::Mud1(bla::Tn5).

References

[1] Beatriz AC, Olfson P and Casadaban MJ. 1984. Plasmid insertion mutagenesis and lac gene fusion with mini-mu bacteriophage transposons. J Bacteriol 158:488-495

[2] Casadaban MJ and Chou J. 1984. in vivo formation of gene fusions encoding hybrid -galactosidase proteins in one step with a transposable Mu-lac transducing phage. Proc Natl Acad Sci 81:535-539

[3] Casadaban MJ and Cohen SN. 1979. Lactose genes fused to exogenous promoters in one step using a Mu-lac bacteriophage: In vivo probe for transcriptional control sequences. Proc Natl Acad Sci 76:4530-4533

[4] Chaconas G, deBrujn FJ, Casadaban MJ, Lupski JR, Kwoh TJ, Harshey RM, DuBow MS and Bukhari AI. 1981. In vitro and in vivo manipulations of bacteriophage Mu DNA: Cloning of Mu ends and construction of mini-Mu's carrying selectable markers. Gene 13:37-46

[5] Groisman EG, Castilho BA, and Casadaban MJ. 1984. In vivo cloning and adjacent gene fusing with a mini-Mu-lac bacteriophage containing a plasmid replicon. Proc Natl Acad Sci 81:1480-1483

[6] Hughes KT and Roth JR. 1984. Conditionally transposition-defective derivation of Mu dI(Amp Lac). J Bacteriol 159:130-137

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Last Update: Thursday June 19 2014

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Eric Kofoid eckofoid at ucdavis.edu