Reviews
Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes
Hannah L Klein1, Kenny K.H. Ang2, Michelle R. Arkin2, Emily C. Beckwitt3,4, Yi-Hsuan Chang5, Jun Fan6, Youngho Kwon7,8, Michael J. Morten1, Sucheta Mukherjee9, Oliver J. Pambos6, Hafez el Sayyed6, Elizabeth S. Thrall10, João P. Vieira-da-Rocha9, Quan Wang11, Shuang Wang12,13, Hsin-Yi Yeh5, Julie S. Biteen14, Peter Chi5,15, Wolf-Dietrich Heyer9,16, Achillefs N. Kapanidis6, Joseph J. Loparo10, Terence R. Strick12,13,17, Patrick Sung7,8, Bennett Van Houten3,18,19, Hengyao Niu11 and Eli Rothenberg1
Mechanistic assays of DNA repair processes are a powerful tools but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.
Pathways of host cell exit by intracellular pathogens
Antje Flieger1,#, Freddy Frischknecht2, Georg Häcker3, Mathias W. Hornef4, Gabriele Pradel5
This review provides an overview of the diverse host cell exit strategies employed by intracellular-living bacterial, fungal, and protozoan pathogens, highlighting the commonalities and system-specific variations of these strategies, and discussing potential microbial molecules involved in host cell exit as targets for future intervention approaches.
Protective roles of ginseng against bacterial infection
Ye-Ram Kim1 and Chul-Su Yang1
This review highlights the antibacterial effects of ginseng against pathogenic bacterial infections, discussing its regulation of pathogenic factors and proposing the therapeutic potential of ginseng as a natural antibacterial drug to address antibiotic resistance and toxicity in the context of global public health challenges.
A Cinderella story: how the vacuolar proteases Pep4 and Prb1 do more than cleaning up the cell’s mass degradation processes
Winnie Kerstens1,2 and Patrick Van Dijck1,2
This review summarizes the expanded roles of the Saccharomyces cerevisiae vacuolar proteases Pep4 and Prb1 in non-vacuolar activities outside of autophagy, such as programmed cell death, protection from harmful protein forms, and gene expression regulation. The potential implications of these findings for fungal biology and drug target discovery, including insights for mammalian cell studies, are highlighted, emphasizing the need for a deeper understanding of these molecular processes.
The biosynthesis of pyoverdines
Michael T. Ringel1 and Thomas Brüser1
This review provides an overview of pyoverdine biosynthesis, emphasizing the distinctive fluorophore shared by various pyoverdines derived from ferribactins and the role of periplasmic processes in the maturation and modification of these siderophores, critical for the growth and colonization of hosts by fluorescent pseudomonads.
Methodologies for in vitro and in vivo evaluation of efficacy of antifungal and antibiofilm agents and surface coatings against fungal biofilms
Patrick Van Dijck1,2,‡, Jelmer Sjollema3,‡, Bruno P.A. Cammue4,5, Katrien Lagrou6,7, Judith Berman8, Christophe d’Enfert9, David R. Andes10,11, Maiken C. Arendrup12-14, Axel A. Brakhage15, Richard Calderone16, Emilia Cantón17, Tom Coenye18,19, Paul Cos20, Leah E. Cowen21, Mira Edgerton22, Ana Espinel-Ingroff23, Scott G. Filler24, Mahmoud Ghannoum25, Neil A.R. Gow26, Hubertus Haas27, Mary Ann Jabra-Rizk28, Elizabeth M. Johnson29, Shawn R. Lockhart30, Jose L. Lopez-Ribot31, Johan Maertens32, Carol A. Munro26, Jeniel E. Nett33, Clarissa J. Nobile34, Michael A. Pfaller35,36, Gordon Ramage19,37, Dominique Sanglard38, Maurizio Sanguinetti39, Isabel Spriet40, Paul E. Verweij41, Adilia Warris42, Joost Wauters43, Michael R. Yeaman44, Sebastian A.J. Zaat45, Karin Thevissen4,*
This article highlights the critical importance of accurate susceptibility testing methods and the discovery of novel antifungal and antibiofilm agents in combating invasive fungal infections associated with biofilm formation on medical devices, thereby emphasizing the need for advancements in medical mycology research to address these complex diseases.
Shepherding DNA ends: Rif1 protects telomeres and chromosome breaks
Gabriele A. Fontana1, Julia K. Reinert1,2, Nicolas H. Thomä1, Ulrich Rass1
This review discusses the conserved mechanisms cells have evolved to protect DNA ends at chromosomal termini and DNA double-strand breaks (DSBs), focusing on the protein Rif1’s roles in telomere homeostasis and DSB repair in eukaryotes. It highlights the intriguing connection between Rif1's involvement in both telomere maintenance and DSB repair, and suggests that excluding end-processing factors may underlie Rif1's diverse biological functions at telomeres and chromosome breaks.
The CRISPR conundrum: evolve and maybe die, or survive and risk stagnation
Jesús García-Martínez1, Rafael D. Maldonado1, Noemí M. Guzmán1 and Francisco J. M. Mojica1,2
In this article García-Martínez et al. cover how the model bacterium Escherichia coli deals with CRISPR-Cas to tackle the major dilemma of evolution versus survival.
Occurrence and potential mechanism of holin-mediated non-lytic protein translocation in bacteria
September 23, 2022
Holins are generally believed to generate large membrane lesions that permit the passage of endolysins across the cytoplasmic membrane of prokaryotes, ultimately resulting in cell wall degradation and cell lysis. However, there are more and more examples known for non-lytic holin-dependent secretion of proteins by bacteria, indicating that holins somehow can transport proteins without causing large membrane lesions. Phage-derived holins can be used for a non-lytic endolysin translocation to permeabilize the cell wall for the passage of secreted proteins. In addition, clostridia, which do not possess the Tat pathway for transport of folded proteins, most likely employ non-lytic holin-mediated transport also for secretion of toxins and bacteriocins that are incompatible with the general Sec pathway. The mechanism for non-lytic holin-mediated transport is (...)
Pirates of the haemoglobin
February 18, 2022
Not all treasure is silver and gold; for pathogenic bacteria, iron is the most precious and the most pillaged of metallic elements. Iron is essential for the survival and growth of all life; however free iron is scarce for bacteria inside human hosts. As a mechanism of defence, humans have evolved ways to store iron so as to render it inaccessible for invading pathogens, such as keeping the metal bound to iron-carrying proteins. For bacteria to survive within humans, they must therefore evolve counters to this defence to compete with these proteins for iron binding, or directly steal iron from them. (...)
Endomembrane remodeling and dynamics in Salmonella infection
December 27, 2021
Salmonellae are bacteria that cause moderate to severe infections in humans, depending on the strain and the immune status of the infected host. These pathogens have the particularity of residing in the cells of the infected host. They are usually found in a vacuolar compartment that the bacteria shape with the help of effector proteins. Following invasion of a eukaryotic cell, the bacterial vacuole undergoes maturation characterized by changes in localization, composition and morphology. In particular, membrane tubules stretching over the microtubule cytoskeleton are formed from the bacterial vacuole. Although these tubules do not occur in all infected cells, they are functionally important and promote intracellular replication. This review focuses on the role and significance of membrane compartment remodeling observed in infected cells and the bacterial and host cell pathways involved.
Lipid and fatty acid metabolism in trypanosomatids
October 6, 2021
This work reviews specific aspects of lipid and fatty acid metabolism in the protozoan parasites T. brucei, T. cruzi, and Leishmania spp., as well as the pathways that have been explored for the development of new chemotherapies.
Understanding the pathogenesis of infectious diseases by single-cell RNA sequencing
August 4, 2021
This work highlights recent remarkable advances in single-cell RNA sequencing technologies and their applications in the investigation of host-pathogen interactions. Current challenges and potential prospects for disease treatment are discussed as well.
Exploring absent protein function in yeast: assaying post translational modification and human genetic variation
July 2, 2021
This review discusses the applicability of yeast systems to investigate absent human protein function with a specific focus on the impact of protein variation on protein-protein interaction modulation.
Mechanisms underlying lactic acid tolerance and its influence on lactic acid production in Saccharomyces cerevisiae
April 14, 2021
This article reviews the manner in which Saccharomyces cerevisiae deals with the accumulation of lactic acid as a singular stress factor as well as in combination with other stresses. In addition, different methods to improve lactic acid tolerance in S. cerevisiae using targeted and non-targeted engineering methods are discussed.
Biofilms by bacterial human pathogens: Clinical relevance – development, composition and regulation – therapeutical strategies
February 1, 2021
This review focuses on bacterial biofilms formed by human pathogens, highlights their relevance for diverse diseases and discusses therapeutical intervention strategies targeting biofilms.
Milestones in Bacillus subtilis sporulation research
November 27, 2020
In this review, the foundational discoveries that shaped the sporulation field are discussed, from its origins to the present day, tracing a chronology that spans more than one hundred eighty years.