Table 1 Top-five along with additional validated (if any) transcriptional regulator targets identified by h-BeReTa for overproducing various compounds in E. coli and its comparison previously existing methods

Acetate

Upregulation

nac, ihfA, tyrR, rpiR, fliZ

tdcA, tdcR, argP [52]

–

Downregulation

cra [31, 59], crp [60], oxyR [17], fur [61], fnr, phoB [62], argP [52]

cra [31, 59]

–

Tyrosine

Upregulation

soxR [63, 64], soxS [63, 64], fadR [65], rcsB, arcA, cra [53]

–

Downregulation

acrR, adiY, gadW, flhD, argP, tyrR [33]

cra [53], tyrR [33], trpR, yebP

–

Fatty acids

Upregulation

fis, fnr, rpiR, yjeB, torR, ompR [66], fadR [4], pdhR [54]

fadR [4]

–

Downregulation

fur, arcA, rcsB, oxyR, cra, crp [67, 68]

pdhR [54], cra, yijC

–

Lycopene

Upregulation

arcA, gadX, fis, ihfA, soxS

soxS

–

Downregulation

rcsB, gadE, rcsA, ihfB, cra

cra, yebP

–

Menaquinone

Upregulation

arcA, nadI, trpR, cra, atoC

–

Downregulation

rob, fnr, creB, tdcR, tdcA

iclR

–

Ethanol

Upregulation

fur, oxyR, glpR, envY, dnaA, arcA [69]

fur

–

Downregulation

rbsE, cpxR, ihfB [56], fnr [56], crp [56]

pdhR [70], cra [71], gntR, kdgR

arcA-pgi, fnr-gntR-pflB-tdcE-tpiA