Deeply branching Bacillota species exhibit atypical Gram-negative staining
Year: 2024
Type: article
Abstract: ABSTRACT The Gram staining method differentiates bacteria based on their cell envelope structure, with the monoderm and diderm cell envelope types traditionally being synonymous with Gram-positive and Gram-negative stain results, respectively. Monoderms have a single phospholipid membrane surrounded by a thick layer of peptidoglycan, while diderms have a lipopolysaccharide outer membrane exterior to a thin peptidoglycan layer. The Bacillota (formerly Firmicutes ) phylum has members with both cell wall types, and recent phylogenetic analyses have shown that monoderm Bacillota evolved from diderm ancestors on multiple occasions. Here, we compiled Gram staining and ultrastructural data for Bacillota species with complete genomes to further investigate the evolution of Gram-positive and Gram-negative cell wall types. The results indicate that many deeply branching lineages at the root of Bacillota phylum stain Gram-negative but do not harbor genes for outer membrane protein or lipopolysaccharide biosynthesis. Phylogenetic reconstructions suggest that several deeply branching Bacillota species have retained a thin peptidoglycan layer in their cell walls, which was inherited from a diderm ancestor. Taxa with this atypical Gram-negative-staining cell wall structure include the thermophilic anaerobe Symbiobacterium thermophilum and members of the Desulfotomaculia, Syntrophamonadia, Desulfitobacteriia, Thermosediminibacteria, and Thermoanaerobacteria . Using Gram-staining results as a proxy for cell wall thickness, our analysis indicates that several independent peptidoglycan thickening events may have occurred in the evolution of the Gram-positive cell envelope. IMPORTANCE In this study, we examined the evolution of bacterial cell envelopes, specifically focusing on Gram-positive and Gram-negative cell wall types in the Bacillota phylum. Our results indicate that certain bacteria can stain Gram-negative despite having a monoderm cell wall structure, thus challenging the conventional interpretation of Gram-staining results. Our observations also question the assumption that Gram-negative staining is always indicative of a diderm structure. These findings have broader implications for understanding how and when cell walls thicken during the evolution of bacterial cell envelopes.
Source: Microbiology Spectrum
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,500
Awards: G301926269, LIFE IS ELECTRIC. THE ELECTRONIC CIRCUITRY IS CATALYZED BY A SMALL SUBSET OF PROTEINS THAT FUNCTION AS SOPHISTICATED NANOMACHINES. CURRENTLY VERY LITTLE IS KNOWN ABOUT THE ORIGIN OF PROTEINS ON EARTH AND THEIR EVOLUTION IN EARLY MICROBIAL LIFE. TO FILL THIS KNOWLEDGE GAP THE ENIGMA RESEARCH PROGRAM WILL CARRY OUT EXPERIMENTAL BIOINFORMATIC DATA-DRIVEN ABDUCTIVE STUDIES TO EXPLORE THE ORIGIN OF CATALYSIS THE EVOLUTION OF PROTEIN STRUCTURES IN MICROBIAL ANCESTORS AND THE CO-EVOLUTION OF PROTEINS AND THE GEOSPHERE THROUGH GEOLOGIC TIME. ENIGMA HAS THREE INTEGRATED RESEARCH THEMES FOCUSED ON UNDERSTANDING THE EVOLUTION OF PROTEINS INVOLVED IN ELECTRON TRANSFER AND ENERGY GENERATION. THEME 1 WILL INVESTIGATE THE SYNTHESIS AND FUNCTION OF METALLOPROTEINS IN PREBIOTIC SYSTEMS. EXTANT MICROBIAL PROTEINS WILL BE ANALYZED TO IDENTIFY THE SIMPLEST STRUCTURES THAT CAN PERFORM ELECTRON TRANSFER REACTIONS. USING DE NOVO COMPUTATIONAL PROTEIN DESIGN SMALL PEPTIDES WILL BE SYNTHESIZED AND CHARACTERIZED TO ELUCIDATE THE EARLIEST BIOCHEMICAL REACTIONS IN THE ORIGIN OF LIFE. THEME 2 WILL EXAMINE THE EMERGENT COMPLEXITY OF METALLOPROTEINS IN MICROBIAL ANCESTORS. NEW COMPUTATIONAL METHODS LINKING PROTEIN STRUCTURE AND PHYLOGENY WILL BE DEVELOPED TO STUDY THE EVOLUTION OF METAL BINDING LIGANDS IN PROTEINS. A STRUCTURAL ALIGNMENT-BASED HOMOLOGY APPROACH WILL BE USED TO IDENTIFY THE OLDEST STRUCTURES IN PROTEINS AND TO TRACE THE EARLY EVOLUTION OF METAL BINDING FOLDS. THEME 3 WILL EXPLORE THE CO-EVOLUTION OF PROTEINS AND THE GEOSPHERE. DEEP-TIME DATA ON THE NATURE AND DISTRIBUTION OF REDOX-SENSITIVE ELEMENTS IN ROCKS AND MINERALS WILL BE INTEGRATED WITH PROTEIN STRUCTURAL DATA IN THE PROTEIN DATA BANK. MINERALOGICAL DATA (E.G. MINERAL COMPOSITION SOLUBILITY AND AGE) WILL BE INCORPORATED INTO GEOCHEMICAL MODELS TO CONSTRAIN THE BIOAVAILABILITY OF METALS OVER GEOLOGIC TIME AND METAL BIOAVAILABILITY DURING ARCHEAN AND PROTEROZOIC ERAS WILL USED TO DATE SPECIFIC POSITIONS IN THE EVOLUTIONARY TREE CONSTRUCTED IN THEME 2. THE THREE ENIGMA RESEARCH THEMES ARE DIRECTLY RELEVANT TO THE MAJOR TOPICS SYNTHESIS AND FUNCTION OF MACROMOLECULES IN THE ORIGIN OF LIFE EARLY LIFE AND INCREASING COMPLEXITY AND CO-EVOLUTION OF LIFE AND THE PHYSICAL ENVIRONMENT IDENTIFIED IN THE 2015 ASTROBIOLOGY SCIENCE STRATEGY. FURTHERMORE THE ENIGMA PROGRAM COMPLEMENTS THE NAI CAN 7 TEAMS ON EXPERIMENTAL MICROBIAL GENOMICS (GEORGIA TECH) AND LIFE ON A DYNAMIC EARLY EARTH (UC RIVERSIDE). THE RESULTS OF THE ENIGMA RESEARCH PROGRAM WILL HELP THE NAI ANSWER A CENTRAL QUESTION IN ASTROBIOLOGY: HOW DID PROTEINS EVOLVE TO BECOME THE CATALYSTS OF LIFE ON EARTH?
OpenAlex ID: W4401714858