Palmer's main research interest is in the processes by which bacteria secrete proteins into their environment. She was one of the co-discoverers of the bacterial Tat protein secretion system. The Tat system is highly unusual because it transports folded proteins of variable sizes across biological membranes while at the same time maintaining the impermeability of the membrane to ions. Palmer has initiated work on a second type of protein transporter– the Type VII secretion system in the human pathogen Staphylococcus aureus. Her group have demonstrated for the first time that the T7SS is involved in interbacterial competition by showing that the S. aureus T7SS secretes a large nuclease toxin, which inhibits the growth of closely related S. aureus strains. Palmer's early career included a post doctoral research position at the University of Dundee where she was a member of Professor David H. Boxer's group in the Department of Biochemistry. At that time Palmer was studying 'Protein FA' - the factor d'association needed for the final step in molybdopterin guanine dinucleotide biosynthesis. Palmer purified the protein and identified it as the product of the mobA gene. From 1993-1996 Palmer was an independent University Research Fellow at the University of Dundee leading a study in to the anaerobic metabolism of Rhodobacter sphaeroides. Indeed, the behaviour of the periplasmic DMSO reductase of Rh. sphaeroides and its E. coli homologue TMAO reductase laid the foundations for Palmer's future research on the Tat pathway. In 1996 Palmer was awarded a Royal Society University Research Fellowship, which was administered by the University of East Anglia in Norwich while Palmer's new research group was based in the Department of Molecular Microbiology at the John Innes Centre. In 2004 Palmer was awarded an MRC Senior Non-Clinical Research Fellowship and was promoted to a Personal Chair in Molecular Microbiology by the University of East Anglia. While in Norwich Palmer began a long collaboration with Professor Ben C. Berks FRS. Together they were awarded the 2002 Microbiology SocietyFleming Prize Lecture for characterisation of the bacterial twin-arginine protein targeting system. In 2007 Palmer was recruited back to the University of Dundee to take up a new position in the College of Life Sciences. Palmer was Head of the Division of Molecular Microbiology at Dundee from 2009-2017 before leaving to join Newcastle University in 2018. She is now Head of the research theme Microbes in Health & Disease, which is part of the Newcastle Biosciences Institute.
