The Middleham handler feels Threading deserves a crack at the York Group Two on Thursday after her scintillating debut success at Goodwood earlier this month.
Nyaleti has been taken out of the Lowther at the confirmation stage and has been handed a chance at the top level at Deauville on Sunday after winning the Group Three Princess Margaret Stakes in convincing style at Ascot last month.
"We've supplemented Threading for the Lowther, so she goes there instead of Nyaleti," Johnston told Press Association Sport.
"She was obviously very impressive first time.
"Unfortunately she wasn't in the Lowther in the first place but we think she's up to it."
As expected, Happy Like A Fool has been added to the Lowther field by American trainer Wesley Ward.
Runner-up in the Queen Mary Stakes, the daughter of Distorted Humor was a late withdrawal from the Molecomb Stakes at Goodwood due to the rain-softened ground.
She was partnered by Frankie Dettori in a racecourse spin at York on Friday morning with the jockey describing her as being "very speedy" and "in good form".
Fifteen juvenile fillies were left in the Lowther at the confirmation stage, with Aidan O'Brien responsible for four of them.
The Ballydoyle trainer's team consists of Actress, Butterscotch, Hence and Chesham Stakes winner September, who has been declared to run at the Curragh on Sunday.
There is a fifth Irish possible in the Ken Condon-trained Mamba Noire.
William Haggas has left in the unbeaten Special Purpose, but she also stood her ground in the Goffs Premier Yearling Conditions Stakes on the same card.