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Microorganisms
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Bacterial Evolution – Molecular Adaptation to Oxygen
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Bacterial Evolution – Molecular Adaptation to Oxygen

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (31 May 2022) | Viewed by 13515

Special Issue Editors

Dr. Mauro Degli Esposti

E-Mail Website
Guest Editor
Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Mexico
Interests: bioenergetics; evolution of mitochondria from bacteria; evolution of respiration; phylogeny of proteobacteria
Dr. Esperanza Martinez-Romero

E-Mail Website
Guest Editor
Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Mexico
Interests: mutualistic symbioses of bacteria with plants and animals, metagenomic and functional genomics approaches, nitrogen-fixing symbioses

Special Issue Information

Dear Colleagues,

These are exciting times for scientists interested in the evolution of life after oxygen became a permanent feature on our planet. The current Special Issue, broadly entitled ‘Bacterial Evolution’, focuses on the molecular adaptation of microorganisms to oxygen and its exploitation to harness bioenergy. The Special Issue intends to bring to the forefront recent advances in the evolutionary aspects of bacteria, especially Proteobacteria living in aquatic environments with limited or gradient oxygen, because such environments resemble those that likely existed when oxygen became available on ancestral earth. It will provide a framework for current and future studies that will uncover the living bacteria that may be closest to the ancestors of mitochondria, the energy-producing organelles of our cells. We already know when (approximately 1.8 billion years ago) and where (in oceanic environments with gradient oxygen) some Alphaproteobacteria underwent the transition to mitochondrial ancestors. This Special Issue will provide a framework to integrate current knowledge on the evolution of aerobic bacteria with the forthcoming discovery of their transition into mitochondria. Hence, mini-reviews, surveys, and original articles that deal with bacterial evolution and any aspect of its relationships with oxygen are more than welcome for this Special Issue. Reviews and communications regarding other topics of bacterial evolution are also welcome to expand the breadth and scientific outreach of the Special Issue.

Dr. Mauro Degli Esposti
Dr. Esperanza Martinez-Romero
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (5 papers)

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Research

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20 pages, 1494 KiB  
Article
New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient
by Miguel Angel Cevallos and Mauro Degli Esposti
Microorganisms 2022, 10(2), 455; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020455 - 16 Feb 2022
Cited by 7 | Viewed by 2912
Abstract
We survey here the Alphaproteobacteria, a large class encompassing physiologically diverse bacteria which are divided in several orders established since 2007. Currently, there is considerable uncertainty regarding the classification of an increasing number of marine metagenome-assembled genomes (MAGs) that remain poorly defined in [...] Read more.
We survey here the Alphaproteobacteria, a large class encompassing physiologically diverse bacteria which are divided in several orders established since 2007. Currently, there is considerable uncertainty regarding the classification of an increasing number of marine metagenome-assembled genomes (MAGs) that remain poorly defined in their taxonomic position within Alphaproteobacteria. The traditional classification of NCBI taxonomy is increasingly complemented by the Genome Taxonomy Database (GTDB), but the two taxonomies differ considerably in the classification of several Alphaproteobacteria, especially from ocean metagenomes. We analyzed the classification of Alphaproteobacteria lineages that are most common in marine environments, using integrated approaches of phylogenomics and functional profiling of metabolic features that define their aerobic metabolism. Using protein markers such as NuoL, the largest membrane subunit of complex I, we have identified new clades of Alphaproteobacteria that are specific to marine niches with steep oxygen gradients (oxycline). These bacteria have relatives among MAGs found in anoxic strata of Lake Tanganyika and together define a lineage that is distinct from either Rhodospirillales or Sneathiellales. We characterized in particular the new ‘oxycline’ clade. Our analysis of Alphaproteobacteria also reveals new clues regarding the ancestry of mitochondria, which likely evolved in oxycline marine environments. Full article
(This article belongs to the Special Issue Bacterial Evolution – Molecular Adaptation to Oxygen)
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Review

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20 pages, 3853 KiB  
Review
A Short Tale of the Origin of Proteins and Ribosome Evolution
by José Arcadio Farías-Rico and Carlos Michel Mourra-Díaz
Microorganisms 2022, 10(11), 2115; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10112115 - 26 Oct 2022
Cited by 1 | Viewed by 2494
Abstract
Proteins are the workhorses of the cell and have been key players throughout the evolution of all organisms, from the origin of life to the present era. How might life have originated from the prebiotic chemistry of early Earth? This is one of [...] Read more.
Proteins are the workhorses of the cell and have been key players throughout the evolution of all organisms, from the origin of life to the present era. How might life have originated from the prebiotic chemistry of early Earth? This is one of the most intriguing unsolved questions in biology. Currently, however, it is generally accepted that amino acids, the building blocks of proteins, were abiotically available on primitive Earth, which would have made the formation of early peptides in a similar fashion possible. Peptides are likely to have coevolved with ancestral forms of RNA. The ribosome is the most evident product of this coevolution process, a sophisticated nanomachine that performs the synthesis of proteins codified in genomes. In this general review, we explore the evolution of proteins from their peptide origins to their folding and regulation based on the example of superoxide dismutase (SOD1), a key enzyme in oxygen metabolism on modern Earth. Full article
(This article belongs to the Special Issue Bacterial Evolution – Molecular Adaptation to Oxygen)
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11 pages, 2198 KiB  
Review
The Genus Iodidimonas: From Its Discovery to Potential Applications
by Seigo Amachi and Takao Iino
Microorganisms 2022, 10(8), 1661; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10081661 - 17 Aug 2022
Cited by 3 | Viewed by 2010
Abstract
The genus Iodidimonas was recently proposed in the class Alphaproteobacteria. Iodidimonas strains are aerobic, mesophilic, neutrophilic, moderately halophilic, and chemo-organotrophic. They were first discovered in natural gas brine water containing a very high level of iodide (I−). They exhibited a unique [...] Read more.
The genus Iodidimonas was recently proposed in the class Alphaproteobacteria. Iodidimonas strains are aerobic, mesophilic, neutrophilic, moderately halophilic, and chemo-organotrophic. They were first discovered in natural gas brine water containing a very high level of iodide (I−). They exhibited a unique phenotypic feature of iodide oxidation to form molecular iodine (I2). Iodidimonas was also enriched and isolated from surface seawater supplemented with iodide, and it is clearer now that their common habitats are those enriched with iodide. In such environments, Iodidimonas species seem to attack microbial competitors with the toxic form I2 to occupy their ecological niche. The iodide-oxidizing enzyme (IOX) purified from the Iodidimonas sp. strain Q-1 exhibited high catalytic efficiency for iodide and consisted of at least two proteins IoxA and IoxC. IoxA is a putative multicopper oxidase with four conserved copper-binding regions but is phylogenetically distinct from other bacterial multicopper oxidases. The IOX/iodide system could be used as a novel enzyme-based antimicrobial system which can efficiently kill Bacillus spores. Furthermore, the IOX/iodide system can be applied to the decolorization of recalcitrant dyes, where iodide may function as a novel inorganic natural redox mediator. Full article
(This article belongs to the Special Issue Bacterial Evolution – Molecular Adaptation to Oxygen)
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29 pages, 9442 KiB  
Review
Evolution of the Inhibitory and Non-Inhibitory ε, ζ, and IF1 Subunits of the F1FO-ATPase as Related to the Endosymbiotic Origin of Mitochondria
by Francisco Mendoza-Hoffmann, Mariel Zarco-Zavala, Raquel Ortega, Heliodoro Celis-Sandoval, Alfredo Torres-Larios and José J. García-Trejo
Microorganisms 2022, 10(7), 1372; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10071372 - 07 Jul 2022
Cited by 6 | Viewed by 2581
Abstract
The F1FO-ATP synthase nanomotor synthesizes >90% of the cellular ATP of almost all living beings by rotating in the “forward” direction, but it can also consume the same ATP pools by rotating in “reverse.” To prevent futile F1 [...] Read more.
The F1FO-ATP synthase nanomotor synthesizes >90% of the cellular ATP of almost all living beings by rotating in the “forward” direction, but it can also consume the same ATP pools by rotating in “reverse.” To prevent futile F1FO-ATPase activity, several different inhibitory proteins or domains in bacteria (ε and ζ subunits), mitochondria (IF1), and chloroplasts (ε and γ disulfide) emerged to block the F1FO-ATPase activity selectively. In this study, we analyze how these F1FO-ATPase inhibitory proteins have evolved. The phylogeny of the α-proteobacterial ε showed that it diverged in its C-terminal side, thus losing both the inhibitory function and the ATP-binding/sensor motif that controls this inhibition. The losses of inhibitory function and the ATP-binding site correlate with an evolutionary divergence of non-inhibitory α-proteobacterial ε and mitochondrial δ subunits from inhibitory bacterial and chloroplastidic ε subunits. Here, we confirm the lack of inhibitory function of wild-type and C-terminal truncated ε subunits of P. denitrificans. Taken together, the data show that ζ evolved to replace ε as the primary inhibitor of the F1FO-ATPase of free-living α-proteobacteria. However, the ζ inhibitory function was also partially lost in some symbiotic α-proteobacteria and totally lost in some strictly parasitic α-proteobacteria such as the Rickettsiales order. Finally, we found that ζ and IF1 likely evolved independently via convergent evolution before and after the endosymbiotic origin mitochondria, respectively. This led us to propose the ε and ζ subunits as tracer genes of the pre-endosymbiont that evolved into the actual mitochondria. Full article
(This article belongs to the Special Issue Bacterial Evolution – Molecular Adaptation to Oxygen)
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17 pages, 741 KiB  
Review
Diversity of Cytochrome c Oxidase Assembly Proteins in Bacteria
by Lars Hederstedt
Microorganisms 2022, 10(5), 926; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10050926 - 28 Apr 2022
Cited by 5 | Viewed by 2841
Abstract
Cytochrome c oxidase in animals, plants and many aerobic bacteria functions as the terminal enzyme of the respiratory chain where it reduces molecular oxygen to form water in a reaction coupled to energy conservation. The three-subunit core of the enzyme is conserved, whereas [...] Read more.
Cytochrome c oxidase in animals, plants and many aerobic bacteria functions as the terminal enzyme of the respiratory chain where it reduces molecular oxygen to form water in a reaction coupled to energy conservation. The three-subunit core of the enzyme is conserved, whereas several proteins identified to function in the biosynthesis of the common family A1 cytochrome c oxidase show diversity in bacteria. Using the model organisms Bacillus subtilis, Corynebacterium glutamicum, Paracoccus denitrificans, and Rhodobacter sphaeroides, the present review focuses on proteins for assembly of the heme a, heme a3, CuB, and CuA metal centers. The known biosynthesis proteins are, in most cases, discovered through the analysis of mutants. All proteins directly involved in cytochrome c oxidase assembly have likely not been identified in any organism. Limitations in the use of mutants to identify and functionally analyze biosynthesis proteins are discussed in the review. Comparative biochemistry helps to determine the role of assembly factors. This information can, for example, explain the cause of some human mitochondrion-based diseases and be used to find targets for new antimicrobial drugs. It also provides information regarding the evolution of aerobic bacteria. Full article
(This article belongs to the Special Issue Bacterial Evolution – Molecular Adaptation to Oxygen)
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