Microbial population dynamics and evolutionary outcomes under extreme energy limitation

Microorganisms commonly inhabit energy-limited ecosystems where cellular maintenance and reproduction is highly constrained. To gain insight into how individuals persist under such conditions, we derived demographic parameters from a collection of 21 heterotrophic bacterial taxa by censusing 100 populations in an effectively closed system for 1,000 d. All but one taxon survived prolonged resource scarcity, yielding estimated times to extinction ranging over four orders of magnitude from 100 to 105 y. Our findings corroborate reports of long-lived bacteria recovered from ancient environmental samples, while providing insight into mechanisms of persistence. As death rates declined over time, lifespan was extended through the scavenging of dead cells. Although reproduction was suppressed in the absence of exogenous resources, populations continued to evolve. Hundreds of mutations were acquired, contributing to genome-wide signatures of purifying selection as well as molecular signals of adaptation. Consistent ecological and evolutionary dynamics indicate that distantly related bacteria respond to energy limitation in a similar and predictable manner, which likely contributes to the stability and robustness of microbial life.

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Microbial population dynamics and evolutionary outcomes under extreme energy-limitation

10.1101/2021.01.25.428163 ◽

2021 ◽

Author(s):

William R. Shoemaker ◽

Stuart E. Jones ◽

Mario E. Muscarella ◽

Megan G. Behringer ◽

Brent K. Lehmkuhl ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Resource Scarcity ◽

Bacterial Populations ◽

Microbial Life ◽

Form Of Life ◽

Diverse Form ◽

Energy Limitation ◽

The Stability ◽

Mechanisms Of Persistence ◽

Insight Into

As the most abundant and diverse form of life on Earth, microorganisms commonly inhabit energy-limited environments where cellular maintenance and growth is highly constrained. To gain insight into how microorganisms persist under such conditions, we derived demographic parameters from a diverse collection of bacteria by censusing 100 populations in a closed system for 1,000 days. All but one taxon survived prolonged resource scarcity, yielding estimated times-to-extinction ranging over four orders of magnitude from 100 – 105 years. These findings corroborate reports of long-lived bacteria that have been recovered from ancient environmental samples, while providing insight into mechanisms of persistence. Critically, we found that as death rates declined over time, lifespan was extended through the scavenging of dead cells. Although growth and reproduction were dramatically suppressed in the absence of an exogenous resource supply, bacterial populations continued to evolve. Hundreds of mutations were acquired, contributing to genome-wide signatures of negative selection as well as molecular signals of adaptation. Remarkable consistency in the ecological and evolutionary dynamics indicate that distantly related bacteria respond to energy-limitation in a similar and predictable manner, which likely contributes to the stability and robustness of microbial life.

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Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2020.1804 ◽

2021 ◽

Vol 288 (1942) ◽

pp. 20201804

Author(s):

Brendan Epstein ◽

Peter Tiffin

Keyword(s):

Positive Selection ◽

Horizontal Transfer ◽

Purifying Selection ◽

Comparative Genomic ◽

N Fixation ◽

Functional Roles ◽

Genome Wide ◽

Rhizobial Symbiosis ◽

Legume Symbiosis ◽

Insight Into

Horizontal transfer (HT) alters the repertoire of symbiosis genes in rhizobial genomes and may play an important role in the on-going evolution of the rhizobia–legume symbiosis. To gain insight into the extent of HT of symbiosis genes with different functional roles (nodulation, N-fixation, host benefit and rhizobial fitness), we conducted comparative genomic and selection analyses of the full-genome sequences from 27 rhizobial genomes. We find that symbiosis genes experience high rates of HT among rhizobial lineages but also bear signatures of purifying selection (low Ka : Ks). HT and purifying selection appear to be particularly strong in genes involved in initiating the symbiosis (e.g. nodulation) and in genome-wide association candidates for mediating benefits provided to the host. These patterns are consistent with rhizobia adapting to the host environment through the loss and gain of symbiosis genes, but not with host-imposed positive selection driving divergence of symbiosis genes through recurring bouts of positive selection.

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Deciphering Evolutionary Dynamics of WRKY I Genes in Rosaceae Species

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2021.801490 ◽

2021 ◽

Vol 9 ◽

Author(s):

Lan Jiang ◽

Yu Chen ◽

De Bi ◽

Yunpeng Cao ◽

Jiucui Tong

Keyword(s):

Evolutionary Dynamics ◽

Developmental Stages ◽

Higher Plants ◽

Expression Patterns ◽

Purifying Selection ◽

Functional Studies ◽

Environmental Selection ◽

Rosaceae Species ◽

The Stability ◽

And Function

WRKY transcription factors participate in various regulation processes at different developmental stages in higher plants. Here, 98 WRKY I genes were identified in seven Rosaceae species. The WRKY I genes are highly enriched in some subgroups and are selectively expanded in Chinese pear [Pyrus bretschneideri (P. bretschneideri)] and apple [Malus domestica (M. domestica)]. By searching for intra-species gene microsynteny, we found the majority of chromosomal segments for WRKY I-containing segments in both P. bretschneideri and M. domestica genomes, while paired segments were hardly identified in the other five genomes. Furthermore, we analyzed the environmental selection pressure of duplicated WRKY I gene pairs, which indicated that the strong purifying selection for WRKY domains may contribute to the stability of its structure and function. The expression patterns of duplication PbWRKY genes revealed that functional redundancy for some of these genes was derived from common ancestry and neo-functionalization or sub-functionalization for some of them. This study traces the evolution of WRKY I genes in Rosaceae genomes and lays the foundation for functional studies of these genes in the future. Our results also show that the rates of gene loss and gain in different Rosaceae genomes are far from equilibrium.

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Evolutionary dynamics of cytoplasmic segregation and fusion: mitochondrial mixing facilitated the evolution of sex at the origin of eukaryotes

10.1101/034116 ◽

2015 ◽

Author(s):

Arunas L. Radzvilavicius

Keyword(s):

Cell Fusion ◽

Evolutionary Dynamics ◽

Purifying Selection ◽

Theoretical Work ◽

Ancestral Population ◽

Evolution Of Sex ◽

Origin And Evolution ◽

Sexual Cell ◽

The Stability

AbstractSexual reproduction is a trait shared by all complex life, but explaining its origin and evolution remains a major theoretical challenge. Virtually all theoretical work on the evolution of sex has focused on the benefits of reciprocal recombination among nuclear genes, paying little attention to the dynamics of mitochondrial genes. Here I develop a mathematical model to study the evolution of alleles inducing cell fusion in an ancestral population of clonal proto-eukaryotes. Mitochondrial mixing masks the detrimental effects of faulty organelles and drives the evolution of sexual cell fusion despite the declining long-term population fitness. Cell-fusion alleles fix under negative epistatic interactions between mitochondrial mutations and strong purifying selection, low mutation load and weak mitochondrial-nuclear associations. I argue that similar conditions could have been maintained throughout the eukaryogenesis, favoring the evolution of sexual cell fusion and meiotic recombination without compromising the stability of the emerging complex cell.

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Nuclear genome-wide associations with mitochondrial heteroplasmy

Science Advances ◽

10.1126/sciadv.abe7520 ◽

2021 ◽

Vol 7 (12) ◽

pp. eabe7520

Author(s):

Priyanka Nandakumar ◽

Chao Tian ◽

Jared O’Connell ◽

David Hinds ◽

Andrew D. Paterson ◽

...

Keyword(s):

Nuclear Genome ◽

Multiple Roles ◽

European Ancestry ◽

Mitochondrial Transcription Factor ◽

Genome Wide ◽

Mtdna Sequence ◽

Nuclear Component ◽

Mitochondrial Transcription Factor A ◽

Mitochondrial Heteroplasmy ◽

The Stability

The role of the nuclear genome in maintaining the stability of the mitochondrial genome (mtDNA) is incompletely known. mtDNA sequence variants can exist in a state of heteroplasmy, which denotes the coexistence of organellar genomes with different sequences. Heteroplasmic variants that impair mitochondrial capacity cause disease, and the state of heteroplasmy itself is deleterious. However, mitochondrial heteroplasmy may provide an intermediate state in the emergence of novel mitochondrial haplogroups. We used genome-wide genotyping data from 982,072 European ancestry individuals to evaluate variation in mitochondrial heteroplasmy and to identify the regions of the nuclear genome that affect it. Age, sex, and mitochondrial haplogroup were associated with the extent of heteroplasmy. GWAS identified 20 loci for heteroplasmy that exceeded genome-wide significance. This included a region overlapping mitochondrial transcription factor A (TFAM), which has multiple roles in mtDNA packaging, replication, and transcription. These results show that mitochondrial heteroplasmy has a heritable nuclear component.

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Genome-wide correlation analysis to identify amplitude regulators of circadian transcriptome output

Scientific Reports ◽

10.1038/s41598-020-78851-9 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Evan S. Littleton ◽

Madison L. Childress ◽

Michaela L. Gosting ◽

Ayana N. Jackson ◽

Shihoko Kojima

Keyword(s):

Clock Genes ◽

Circadian System ◽

Average Level ◽

Relative Amplitude ◽

Critical Component ◽

Period 2 ◽

Genome Wide ◽

Mouse Tissues ◽

Rhythmic Gene ◽

Insight Into

AbstractCell-autonomous circadian system, consisting of core clock genes, generates near 24-h rhythms and regulates the downstream rhythmic gene expression. While it has become clear that the percentage of rhythmic genes varies among mouse tissues, it remains unclear how this variation can be generated, particularly when the clock machinery is nearly identical in all tissues. In this study, we sought to characterize circadian transcriptome datasets that are publicly available and identify the critical component(s) involved in creating this variation. We found that the relative amplitude of 13 genes and the average level of 197 genes correlated with the percentage of cycling genes. Of those, the correlation of Rorc in both relative amplitude and the average level was one of the strongest. In addition, the level of Per2AS, a novel non-coding transcript that is expressed at the Period 2 locus, was also linearly correlated, although with a much lesser degree compared to Rorc. Overall, our study provides insight into how the variation in the percentage of clock-controlled genes can be generated in mouse tissues and suggests that Rorc and potentially Per2AS are involved in regulating the amplitude of circadian transcriptome output.

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Genome-Wide Identification of Soybean ABC Transporters Relate to Aluminum Toxicity

International Journal of Molecular Sciences ◽

10.3390/ijms22126556 ◽

2021 ◽

Vol 22 (12) ◽

pp. 6556

Author(s):

Junjun Huang ◽

Xiaoyu Li ◽

Xin Chen ◽

Yaru Guo ◽

Weihong Liang ◽

...

Keyword(s):

Gene Expression ◽

Abc Transporters ◽

Developmental Stages ◽

Aluminum Toxicity ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Purifying Selection ◽

Biotic Stresses ◽

Genome Wide ◽

New Germplasm

ATP-binding cassette (ABC) transporter proteins are a gene super-family in plants and play vital roles in growth, development, and response to abiotic and biotic stresses. The ABC transporters have been identified in crop plants such as rice and buckwheat, but little is known about them in soybean. Soybean is an important oil crop and is one of the five major crops in the world. In this study, 255 ABC genes that putatively encode ABC transporters were identified from soybean through bioinformatics and then categorized into eight subfamilies, including 7 ABCAs, 52 ABCBs, 48 ABCCs, 5 ABCDs, 1 ABCEs, 10 ABCFs, 111 ABCGs, and 21 ABCIs. Their phylogenetic relationships, gene structure, and gene expression profiles were characterized. Segmental duplication was the main reason for the expansion of the GmABC genes. Ka/Ks analysis suggested that intense purifying selection was accompanied by the evolution of GmABC genes. The genome-wide collinearity of soybean with other species showed that GmABCs were relatively conserved and that collinear ABCs between species may have originated from the same ancestor. Gene expression analysis of GmABCs revealed the distinct expression pattern in different tissues and diverse developmental stages. The candidate genes GmABCB23, GmABCB25, GmABCB48, GmABCB52, GmABCI1, GmABCI5, and GmABCI13 were responsive to Al toxicity. This work on the GmABC gene family provides useful information for future studies on ABC transporters in soybean and potential targets for the cultivation of new germplasm resources of aluminum-tolerant soybean.

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Bioinspired organometallic chemistry

Pure and Applied Chemistry ◽

10.1351/pac200274010115 ◽

2002 ◽

Vol 74 (1) ◽

pp. 115-122 ◽

Cited By ~ 24

Author(s):

Lanny S. Liebeskind ◽

Jiri Srogl ◽

Cecile Savarin ◽

Concepcion Polanco

Keyword(s):

Organometallic Chemistry ◽

Refractory Metal ◽

Redox Active ◽

The Stability ◽

New Procedures ◽

Sulfur Containing ◽

Insight Into

Given the stability of the bond between a mercaptide ligand and various redox-active metals, it is of interest that Nature has evolved significant metalloenzymatic processes that involve key interactions of sulfur-containing functionalities with metals such as Ni, Co, Cu, and Fe. From a chemical perspective, it is striking that these metals can function as robust biocatalysts in vivo, even though they are often "poisoned" as catalysts in vitro through formation of refractory metal thiolates. Insight into the nature of this chemical discrepancy is under study in order to open new procedures in synthetic organic and organometallic chemistry.

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Genome-wide characterization and expression profiling of B3 superfamily during ethylene-induced flowering in pineapple (Ananas comosus L.)

BMC Genomics ◽

10.1186/s12864-021-07854-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Cheng Cheng Ruan ◽

Zhe Chen ◽

Fu Chu Hu ◽

Wei Fan ◽

Xiang He Wang ◽

...

Keyword(s):

Development Process ◽

Chromosomal Localization ◽

Purifying Selection ◽

Ananas Comosus ◽

Pcr Analysis ◽

Flower Bud ◽

Genome Wide ◽

Localization Analysis ◽

Ethephon Treatment ◽

Differentiation Period

Abstract Background The B3 superfamily (B3s) represents a class of large plant-specific transcription factors, which play diverse roles in plant growth and development process including flowering induction. However, identification and functional surveys of B3 superfamily have not been reported in ethylene-induced pineapple flowering (Ananas comosus). Results 57 B3 genes containing B3 domain were identified and phylogenetically classified into five subfamilies. Chromosomal localization analysis revealed that 54 of 57 AcB3s were located on 21 Linkage Groups (LG). Collinearity analysis demonstrated that the segmental duplication was the main event in the evolution of B3 gene superfamily, and most of them were under purifying selection. The analysis of cis-element composition suggested that most of these genes may have function in response to abscisic acid, ethylene, MeJA, light, and abiotic stress. qRT-PCR analysis of 40 AcB3s containing ethylene responsive elements exhibited that the expression levels of 35 genes were up-regulated within 1 d after ethephon treatment and some were highly expressed in flower bud differentiation period in stem apex, such as Aco012003, Aco019552 and Aco014401. Conclusion This study provides a basic information of AcB3s and clues for involvement of some AcB3s in ethylene-induced flowering in pineapple.

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Genome-wide identification of chitinase genes in Thalassiosira pseudonana and analysis of their expression under abiotic stresses

BMC Plant Biology ◽

10.1186/s12870-021-02849-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Haomiao Cheng ◽

Zhanru Shao ◽

Chang Lu ◽

Delin Duan

Keyword(s):

Abiotic Stresses ◽

Chitinase Activity ◽

Thalassiosira Pseudonana ◽

Centric Diatom ◽

Carbon And Nitrogen ◽

Genome Wide ◽

Duplication Events ◽

The Many ◽

Chitinase Genes ◽

Insight Into

Abstract Background The nitrogen-containing polysaccharide chitin is the second most abundant biopolymer on earth and is found in the cell walls of diatoms, where it serves as a scaffold for biosilica deposition. Diatom chitin is an important source of carbon and nitrogen in the marine environment, but surprisingly little is known about basic chitinase metabolism in diatoms. Results Here, we identify and fully characterize 24 chitinase genes from the model centric diatom Thalassiosira pseudonana. We demonstrate that their expression is broadly upregulated under abiotic stresses, despite the fact that chitinase activity itself remains unchanged, and we discuss several explanations for this result. We also examine the potential transcriptional complexity of the intron-rich T. pseudonana chitinase genes and provide evidence for two separate tandem duplication events during their evolution. Conclusions Given the many applications of chitin and chitin derivatives in suture production, wound healing, drug delivery, and other processes, new insight into diatom chitin metabolism has both theoretical and practical value.

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