Identification of new DNA-associated proteins from Waddlia chondrophila

Barsy, Marie de; Herrgott, Lucas; Martin, Virginie; Pillonel, Trestan; Viollier, Patrick H.; Greub, Gilbert

doi:10.1038/s41598-019-40732-1

Cited by 6 publications

(4 citation statements)

References 51 publications

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“…Owing to the highly conserved intracellular lifestyle, investigating environmental chlamydiae has contributed to a better understanding of the basic biology of all chlamydiae. This includes (i) the discovery of peptidoglycan, which was surprising because chlamydiae have been considered peptidoglycan-less bacteria for decades [7,8]; (ii) the characterization of their FtsZ-less mode of cell division [5,7,8,67,68]; (iii) the demonstration of metabolic activity in the infectious EBs, which have traditionally been considered metabolically inert [4,69]; (iv) the identification of highly conserved transcription factors involved in the exploitation of the intracellular niche [70][71][72]; and (v) the analysis of their biphasic metabolism that involves a shift regarding carbon metabolism and energy generation during differentiation from EBs to RBs and back [69,73,74].…”

Section: Clues About Basic Chlamydial Biology From Environmental Chlamydiaementioning

confidence: 99%

Chlamydiae in the Environment

Collingro

Köstlbacher

Horn

2020

Trends in Microbiology

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Chlamydiae have been known for more than a century as major pathogens of humans. Yet they are also found ubiquitously in the environment where they thrive within protists and in an unmatched wide range of animals. This review summarizes recent advances in understanding chlamydial diversity and distribution in nature. Studying these environmental chlamydiae provides a novel perspective on basic chlamydial biology and evolution. A picture is beginning to emerge with chlamydiae representing one of the evolutionarily most ancient and successful groups of obligate intracellular bacteria. A Chlamydia for Every EukaryoteChlamydiae are a major cause of eye infections (trachoma) and sexually transmitted disease, being responsible for an estimated 2 million and 130 million infections worldwide per year, respectively [1]. They were originally described as a small, well-separated group of bacteria infecting humans and birds through an unusual and strictly intracellular developmental cycle. During the past two decades, novel chlamydiae have been discovered within protists such as amoebae, and in diverse animal hosts [2,3]. Interchangeably referred to as chlamydia-like organisms (CLOs) or environmental chlamydiae (see Glossary), studying these environmental microbes revealed striking similarities with, and unexpected differences to, the wellknown human pathogens Chlamydia trachomatis, C. pneumoniae, and C.psittaci [2][3][4].A number of review articles have addressed the discovery of these novel chlamydiae, selected aspects of their biology, their interaction with hosts, and their potential role as human and animal pathogens [2][3][4][5][6][7][8][9][10][11][12][13][14]. Here, we focus on accumulating evidence for a widespread occurrence of chlamydiae in diverse environments, as members of various microbiomes, and in a wide range of hoststogether indicating that chlamydiae are indeed ubiquitous in nature. Following the paradigm that (chlamydial) pathogens once originated from environmental bacteria, we highlight recent environmental chlamydia research about fundamental aspects of chlamydial biology, and we show how studying these environmental representatives provides a framework for understanding the evolution of this unique group of intracellular microbes. Microbiome Research Recovers Novel ChlamydiaeOwing to their obligate intracellular lifestyle, chlamydiae are inherently difficult to study and their retrieval directly from environmental samples is challenging. The application of next-generation sequencing techniques in amplicon, single-cell, and metagenome studies has thus been instrumental in investigating chlamydial diversity and biology [15]. Recent technological advances enabled deep sampling as well as deep sequencing, facilitating the recovery of rare taxa in diverse microbiomes and environments. This revealed a hitherto underestimated broad distribution of chlamydiae in nature and a surprisingly high abundance in some habitats [10,[16][17][18][19][20][21][22]. Diversity of Chlamydiae in the EnvironmentRepresentatives...

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Section: Clues About Basic Chlamydial Biology From Environmental Chlamydiaementioning

confidence: 99%

Chlamydiae in the Environment

Collingro

Köstlbacher

Horn

2020

Trends in Microbiology

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“…Vero cells were selected as host cells, since they are better suited for drug susceptibility tests than amoebae, which harbor efflux machineries that protect them from chemical compounds [36]. Moreover, several studies already used Vero cells for treatment of W. chondrophila with different drugs [18,53,54]. Therefore, Vero cells were infected with Waddlia and treated with drug concentrations ranging from 8 to 1000 µg/mL.…”

Section: Stress Stimuli Induce Different Morphological Subtypes Of Abmentioning

confidence: 99%

Diverse Stress-Inducing Treatments cause Distinct Aberrant Body Morphologies in the Chlamydia-Related Bacterium, Waddlia chondrophila

et al. 2020

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Chlamydiae, such as Chlamydia trachomatis and Chlamydia pneumoniae, can cause chronic infections. It is believed that persistent forms called aberrant bodies (ABs) might be involved in this process. AB formation seems to be a common trait of all members of the Chlamydiales order and is caused by distinct stress stimuli, such as β-lactam antibiotics or nutrient starvation. While the diverse stimuli inducing ABs are well described, no comprehensive morphological characterization has been performed in Chlamydiales up to now. We thus infected mammalian cells with the Chlamydia-related bacterium Waddlia chondrophila and induced AB formation using different stimuli. Their morphology, differences in DNA content and in gene expression were assessed by immunofluorescence, quantitative PCR, and reverse transcription PCR, respectively. All stimuli induced AB formation. Interestingly, we show here for the first time that the DNA gyrase inhibitor novobiocin also caused appearance of ABs. Two distinct patterns of ABs could be defined, according to their morphology and number: (i) small and multiple ABs versus (ii) large and rare ABs. DNA replication of W. chondrophila was generally not affected by the different treatments. Finally, no correlation could be observed between specific types of ABs and expression patterns of mreB and rodZ genes.

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“…Identification of nucleic acid-binding proteins is one of the most important tasks in molecular biology. Currently, nucleic acid-binding proteins can be identified and further characterized by several experimental techniques, including pull-down assays [ 2 , 3 ], yeast one-hybrid system [ 4 , 5 ], electrophoretic mobility shift assays [ 6 , 7 ], chromatin immunoprecipitation [ 8 , 9 ], and by other specialized techniques [ 10 , 11 ]. However, it is time-consuming and expensive to identify nucleic acid-binding proteins by experimental approaches [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

Amino Acid Composition in Various Types of Nucleic Acid-Binding Proteins

Bartas

Červeň

Guziurová

et al. 2021

IJMS

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Nucleic acid-binding proteins are traditionally divided into two categories: With the ability to bind DNA or RNA. In the light of new knowledge, such categorizing should be overcome because a large proportion of proteins can bind both DNA and RNA. Another even more important features of nucleic acid-binding proteins are so-called sequence or structure specificities. Proteins able to bind nucleic acids in a sequence-specific manner usually contain one or more of the well-defined structural motifs (zinc-fingers, leucine zipper, helix-turn-helix, or helix-loop-helix). In contrast, many proteins do not recognize nucleic acid sequence but rather local DNA or RNA structures (G-quadruplexes, i-motifs, triplexes, cruciforms, left-handed DNA/RNA form, and others). Finally, there are also proteins recognizing both sequence and local structural properties of nucleic acids (e.g., famous tumor suppressor p53). In this mini-review, we aim to summarize current knowledge about the amino acid composition of various types of nucleic acid-binding proteins with a special focus on significant enrichment and/or depletion in each category.

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Identification of new DNA-associated proteins from Waddlia chondrophila

Cited by 6 publications

References 51 publications

Chlamydiae in the Environment

Chlamydiae in the Environment

Diverse Stress-Inducing Treatments cause Distinct Aberrant Body Morphologies in the Chlamydia-Related Bacterium, Waddlia chondrophila

Amino Acid Composition in Various Types of Nucleic Acid-Binding Proteins

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