scholarly journals Homology between the flagellar export apparatus and ATP synthetase: evidence from synteny predating the Last Universal Common Ancestor

2021 ◽  
Author(s):  
Nicholas J. Matzke ◽  
Angela Lin ◽  
Micaella Stone ◽  
Matthew A. B. Baker
Keyword(s):  
Gene Order ◽  
Common Ancestor ◽  
Phylogenetic Distance ◽  
Last Universal Common Ancestor ◽  
Universal Common Ancestor ◽  
Atpase Gene ◽  
Type 3 Secretion System ◽  
Conserved Gene ◽  
And Function ◽  
Type 3

AbstractEvidence of homology between proteins in the ATP synthetase and the bacterial flagellar motor (BFM) has been accumulating since the 1980s. Specifically, the BFM’s Type 3 Secretion System (T3SS) export apparatus FliH, FliI, and FliJ are considered homologous to FO-b + F1-δ, F1-α/β, and F1-γ, and have similar structure and interactions. We review the discoveries that advanced the homology hypothesis and then conduct a further test by examining gene order in the two systems and their relatives. Conservation of gene order, or synteny, is often observed between closely related prokaryote species, but usually degrades with phylogenetic distance. As a result, observed conservation of synteny over vast phylogenetic distances can be evidence of shared ancestral coexpression, interaction, and function. We constructed a gene order dataset by examining the order of fliH, fliI, and fliJ genes across the phylogenetic breadth of flagellar and nonflagellar T3SS. We compared this to published surveys of gene order in the F1FO-ATP synthetase, its N-ATPase relatives, and the bacterial/archaeal V- and A-type ATPases. Strikingly, the fliHIJ gene order was deeply conserved, with the few exceptions appearing derived, and exactly matching the widely conserved F-ATPase gene order atpFHAG, coding for subunits b-δ-α-γ. The V/A-type ATPases have a similar conserved gene order shared for homologous components. Our results further strengthen the argument for homology between these systems, and suggest a rare case of synteny conserved over billions of years, dating back to well before the Last Universal Common Ancestor (LUCA).

scholarly journals A New Analysis of Archaea–Bacteria Domain Separation: Variable Phylogenetic Distance and the Tempo of Early Evolution

2020 ◽  
Vol 37 (8) ◽  
pp. 2332-2340 ◽  
Author(s):  
Sarah J Berkemer ◽  
Shawn E McGlynn
Keyword(s):  
Phylogenetic Trees ◽  
Molecular Phylogenetics ◽  
Common Ancestor ◽  
Rapid Evolution ◽  
Biological Evolution ◽  
Protein Family ◽  
Phylogenetic Distance ◽  
Protein Families ◽  
Last Universal Common Ancestor ◽  
Universal Common Ancestor

Abstract Comparative genomics and molecular phylogenetics are foundational for understanding biological evolution. Although many studies have been made with the aim of understanding the genomic contents of early life, uncertainty remains. A study by Weiss et al. (Weiss MC, Sousa FL, Mrnjavac N, Neukirchen S, Roettger M, Nelson-Sathi S, Martin WF. 2016. The physiology and habitat of the last universal common ancestor. Nat Microbiol. 1(9):16116.) identified a number of protein families in the last universal common ancestor of archaea and bacteria (LUCA) which were not found in previous works. Here, we report new research that suggests the clustering approaches used in this previous study undersampled protein families, resulting in incomplete phylogenetic trees which do not reflect protein family evolution. Phylogenetic analysis of protein families which include more sequence homologs rejects a simple LUCA hypothesis based on phylogenetic separation of the bacterial and archaeal domains for a majority of the previously identified LUCA proteins (∼82%). To supplement limitations of phylogenetic inference derived from incompletely populated orthologous groups and to test the hypothesis of a period of rapid evolution preceding the separation of the domains, we compared phylogenetic distances both within and between domains, for thousands of orthologous groups. We find a substantial diversity of interdomain versus intradomain branch lengths, even among protein families which exhibit a single domain separating branch and are thought to be associated with the LUCA. Additionally, phylogenetic trees with long interdomain branches relative to intradomain branches are enriched in information categories of protein families in comparison to those associated with metabolic functions. These results provide a new view of protein family evolution and temper claims about the phenotype and habitat of the LUCA.

scholarly journals SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nika Pende ◽  
Adrià Sogues ◽  
Daniela Megrian ◽  
Anna Sartori-Rupp ◽  
Patrick England ◽  
...  
Keyword(s):  
Cell Division ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Super Resolution ◽  
Binding Mode ◽  
Last Universal Common Ancestor ◽  
Division Plane ◽  
Multiple Factors ◽  
Universal Common Ancestor ◽  
Super Resolution Microscopy

AbstractMost archaea divide by binary fission using an FtsZ-based system similar to that of bacteria, but they lack many of the divisome components described in model bacterial organisms. Notably, among the multiple factors that tether FtsZ to the membrane during bacterial cell constriction, archaea only possess SepF-like homologs. Here, we combine structural, cellular, and evolutionary analyses to demonstrate that SepF is the FtsZ anchor in the human-associated archaeon Methanobrevibacter smithii. 3D super-resolution microscopy and quantitative analysis of immunolabeled cells show that SepF transiently co-localizes with FtsZ at the septum and possibly primes the future division plane. M. smithii SepF binds to membranes and to FtsZ, inducing filament bundling. High-resolution crystal structures of archaeal SepF alone and in complex with the FtsZ C-terminal domain (FtsZCTD) reveal that SepF forms a dimer with a homodimerization interface driving a binding mode that is different from that previously reported in bacteria. Phylogenetic analyses of SepF and FtsZ from bacteria and archaea indicate that the two proteins may date back to the Last Universal Common Ancestor (LUCA), and we speculate that the archaeal mode of SepF/FtsZ interaction might reflect an ancestral feature. Our results provide insights into the mechanisms of archaeal cell division and pave the way for a better understanding of the processes underlying the divide between the two prokaryotic domains.

scholarly journals Interaction of Escherichia coli O157:H7 with Leafy Green Produce

2009 ◽  
Vol 72 (7) ◽  
pp. 1531-1537 ◽  
Author(s):  
JUAN XICOHTENCATL-CORTES ◽  
ETHEL SÁNCHEZ CHACÓN ◽  
ZEUS SALDAÑA ◽  
ENRIQUE FREER ◽  
JORGE A. GIRÓN
Keyword(s):  
Escherichia Coli ◽  
Diarrheal Disease ◽  
Foodborne Pathogen ◽  
Enterohemorrhagic Escherichia Coli ◽  
Animal Products ◽  
Atpase Gene ◽  
Type 3 Secretion System ◽  
Human Infections ◽  
Type 3

Enterohemorrhagic Escherichia coli (EHEC) is a foodborne pathogen responsible for human diarrheal disease. EHEC lives in the intestinal tract of cattle and other farm and wild animals, which may be the source of environmental contamination particularly of agricultural fields. Human infections are associated with consumption of tainted animal products and fresh produce. How the bacteria interact with the plant phyllosphere and withstand industrial decontamination remain to be elucidated. The goals of the present study were to investigate the environmental conditions and surface structures that influence the interaction of EHEC O157:H7 with baby spinach and lettuce leaves in vitro. Independently of the production of Shiga toxin, EHEC O157:H7 colonizes the leaf surface via flagella and the type 3 secretion system (T3SS). Ultrastructural analysis of EHEC-infected leafy greens revealed the presence of flagellated bacteria, and mutation of the fliC flagellin gene in EHEC EDL933 rendered the bacteria significantly less adherent, suggesting the involvement of flagella in the bacteria-leaf interaction. EDL933 mutated in the escN (ATPase) gene associated with the function of the T3SS but not in the eae (intimin adhesin) gene required for adherence to host intestinal cells had significantly reduced adherence compared with that of the parental strain. The data suggest a compelling role of flagella and the T3SS in colonization of leafy green produce. Colonization of salad leaves by EHEC strains may be a strategy that ensures survival of these bacteria in the environment and allows transmission to the human host.

scholarly journals Origin of Life

2021 ◽  
Vol 83 (2) ◽  
pp. 76-79
Author(s):  
Cristina Sousa
Keyword(s):  
Origin Of Life ◽  
Common Ancestor ◽  
Scientific Evidence ◽  
Recent Common Ancestor ◽  
Last Universal Common Ancestor ◽  
Most Recent Common Ancestor ◽  
Universal Common Ancestor ◽  
The Origin Of Life

The origin of life is one of the most interesting and challenging questions in biology. This article discusses relevant contemporary theories and hypotheses about the origin of life, recent scientific evidence supporting them, and the main contributions of several scientists of different nationalities and specialties in different disciplines. Also discussed are several ideas about the characteristics of the most recent common ancestor, also called the “last universal common ancestor” (or LUCA), including cellular status (unicellular or community) and homogeneity level.

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