Parallel molecular mechanisms for enzyme temperature adaptation

Science ◽  
2021 ◽  
Vol 371 (6533) ◽  
pp. eaay2784
Author(s):  
Margaux M. Pinney ◽  
Daniel A. Mokhtari ◽  
Eyal Akiva ◽  
Filip Yabukarski ◽  
David M. Sanchez ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Interaction Networks ◽  
Temperature Adaptation ◽  
Mechanistic Studies ◽  
Sequence Analyses ◽  
Evolutionary Mechanisms ◽  
Ketosteroid Isomerase ◽  
Physical Mechanisms ◽  
Bacterial Enzyme ◽  
Enzyme Families

The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. We identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.

scholarly journals Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus

2021 ◽  
Author(s):  
Zhilin Yuan ◽  
Irina S. Druzhinina ◽  
John G. Gibbons ◽  
Zhenhui Zhong ◽  
Yves Van de Peer ◽  
...  
Keyword(s):  
Membrane Trafficking ◽  
Molecular Mechanisms ◽  
Genomic Island ◽  
Population Genomics ◽  
Growth Yield ◽  
Fixation Index ◽  
Nucleotide Polymorphisms ◽  
Evolutionary Mechanisms ◽  
Melanin Biosynthesis ◽  
Two Populations

AbstractUnderstanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics. Based on genome-wide Fst (pairwise fixation index) and Vst analyses, which compared the variance in allele frequencies of single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), respectively, we found a high level of genetic differentiation between two populations. CNV patterns revealed population-specific expansions and contractions. Interestingly, we identified a ~20 kbp genomic island of high divergence with a strong sign of positive selection. This region contains a melanin-biosynthetic polyketide synthase gene cluster linked to six additional genes likely involved in biosynthesis, membrane trafficking, regulation, and localization of melanin. Differences in growth yield and melanin biosynthesis between the two populations grown under 2% NaCl stress suggested that this genomic island contributes to the observed differences in melanin accumulation. Our findings provide a better understanding of the genetic and evolutionary mechanisms underlying the adaptation to saline conditions of the L. rhizohalophila–S. salsa symbiosis.

Molecules from the Microbiome

2021 ◽  
Vol 90 (1) ◽  
Author(s):  
Emilee E. Shine ◽  
Jason M. Crawford
Keyword(s):  
Small Molecules ◽  
Molecular Mechanisms ◽  
System Development ◽  
Human Microbiome ◽  
Host Responses ◽  
Annual Review ◽  
Publication Date ◽  
Mechanistic Studies ◽  
Immune System Development ◽  
Interdisciplinary Approaches

The human microbiome encodes a second genome that dwarfs the genetic capacity of the host. Microbiota-derived small molecules can directly target human cells and their receptors or indirectly modulate host responses through functional interactions with other microbes in their ecological niche. Their biochemical complexity has profound implications for nutrition, immune system development, disease progression, and drug metabolism, as well as the variation in these processes that exists between individuals. While the species composition of the human microbiome has been deeply explored, detailed mechanistic studies linking specific microbial molecules to host phenotypes are still nascent. In this review, we discuss challenges in decoding these interaction networks, which require interdisciplinary approaches that combine chemical biology, microbiology, immunology, genetics, analytical chemistry, bioinformatics, and synthetic biology. We highlight important classes of microbiota-derived small molecules and notable examples. An understanding of these molecular mechanisms is central to realizing the potential of precision microbiome editing in health, disease, and therapeutic responses. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Temporal Distinction between Male and Female Floral Organ Development in Nicotiana tabacum cv. Xanthi (Solanaceae)

Plants ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 127
Author(s):  
Hongli Chang ◽  
Fengjie Sun
Keyword(s):  
Nicotiana Tabacum ◽  
Molecular Mechanisms ◽  
Pollen Grains ◽  
Floral Organ ◽  
Evolutionary Mechanisms ◽  
Tetrad Stage ◽  
Flower Primordia ◽  
Future Studies ◽  
Carpel Development ◽  
Solid Foundation

Early floral developmental investigations provide crucial evidence for phylogenetic and molecular studies of plants. The developmental and evolutionary mechanisms underlying the variations in floral organs are critical for a thorough understanding of the diversification of flowers. Ontogenetic comparisons between anthers and pistil within single flowers were characterized over time in Nicotiana tabacum cv. Xanthi. The ages of 42 tobacco flower or flower primordia were estimated using corolla growth analysis. Results showed that the protodermal layer in carpel primordia contributes to carpel development by both anticlinal and periclinal divisions. Periclinal divisions in the hypodermal layer of the placenta were observed around 4.8 ± 1.3 days after the formation of early carpel primordia (ECP) and ovule initiation occurred 10.0 ± 0.5 days after ECP. Meiosis in anthers and ovules began about 8.9 ± 1.1 days and 14.4 ± 1.3 days after ECP, respectively. Results showed an evident temporal distinction between megasporogenesis and microsporogenesis. Flower ages spanned a 17-day interval, starting with flower primordia containing the ECP and anther primordia to the tetrad stage of meiosis in megasporocytes and the bicellular stage in pollen grains. These results establish a solid foundation for future studies in order to identify the developmental and molecular mechanisms responsible for the mating system in tobacco.

Evolutionary Analyses of Protein Interaction Networks

2009 ◽  
pp. 169-181 ◽  
Author(s):  
Takashi Makino ◽  
Aoife McLysaght
Keyword(s):  
Molecular Evolution ◽  
Comparative Genomics ◽  
Protein Interaction ◽  
Protein Interaction Networks ◽  
Evolutionary Rates ◽  
Interaction Networks ◽  
Evolutionary Mechanisms ◽  
Ancestral Gene ◽  
Protein Protein Interaction ◽  
A Genome

This chapter introduces evolutionary analyses of protein interaction networks and of proteins as components of the networks. The authors show relationships between proteins in the networks and their evolutionary rates. For understanding protein-protein interaction (PPI) divergence, duplicated genes are often compared because they are derived from a common ancestral gene. In order to reveal evolutionary mechanisms acting on the interactome it is necessary to compare PPIs across species. Investigation of co-localization of interacting genes in a genome shows that PPIs have an important role in the maintenance of a physical link between neighboring genes. The purpose of this chapter is to introduce methodologies for analyzing PPI data and to describe molecular evolution and comparative genomics insights gained from such studies.

scholarly journals The MHC Class Ia Genes in Chenfu’s Treefrog (Zhangixalus chenfui) Evolved via Gene Duplication, Recombination, and Selection

Animals ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 34
Author(s):  
Hu Chen ◽  
Siqi Huang ◽  
Ye Jiang ◽  
Fuyao Han ◽  
Qingyong Ni ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Positive Selection ◽  
Phylogenetic Relationships ◽  
Molecular Mechanisms ◽  
Coding Region ◽  
Evolutionary Mechanisms ◽  
Evolutionary Patterns ◽  
Mhc Genes ◽  
Mhc Class Ia ◽  
Related Proteins

The molecular mechanisms underlying the evolution of adaptive immunity-related proteins can be deduced by a thorough examination of the major histocompatibility complex (MHC). Currently, in vertebrates, there is a relatively large amount of research on MHCs in mammals and birds. However, research related to amphibian MHC genes and knowledge about the evolutionary patterns is limited. This study aimed to isolate the MHC class I genes from Chenfu’s Treefrog (Zhangixalus chenfui) and reveal the underlying evolutionary processes. A total of 23 alleles spanning the coding region of MHC class Ia genes were identified in 13 individual samples. Multiple approaches were used to test and identify recombination from the 23 alleles. Amphibian MHC class Ia alleles, from NCBI, were used to construct the phylogenetic relationships in MEGA. Additionally, the partition strategy was adopted to construct phylogenetic relationships using MrBayes and MEGA. The sites of positive selection were identified by FEL, PAML, and MEME. In Chenfu’s Treefrog, we found that: (1) recombination usually takes place between whole exons of MHC class Ia genes; (2) there are at least 3 loci for MHC class Ia, and (3) the diversity of genes in MHC class Ia can be attributed to recombination, gene duplication, and positive selection. We characterized the evolutionary mechanisms underlying MHC class Ia genes in Chenfu’s Treefrog, and in so doing, broadened the knowledge of amphibian MHC systems.

scholarly journals Insights on protein thermal stability: a graph representation of molecular interactions

2018 ◽  
Author(s):  
Mattia Miotto ◽  
Pier Paolo Olimpieri ◽  
Lorenzo Di Rienzo ◽  
Francesco Ambrosetti ◽  
Pietro Corsi ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Molecular Mechanisms ◽  
Interaction Networks ◽  
Graph Representation ◽  
Weighted Graphs ◽  
Native Structure ◽  
Wide Range ◽  
Potential Applications ◽  
Free Network ◽  
Native Fold

ABSTRACTUnderstanding the molecular mechanisms of thermal stability is a challenge in protein biology. Indeed, knowing the temperature at which proteins are stable has important theoretical implications, which are intimately linked with properties of the native fold, and a wide range of potential applications from drug design to the optimization of enzyme activity.Here, we present a novel graph-theoretical framework to assess thermal stability based on the structure without any a priori information. In our approach we describe proteins as energy-weighted graphs and compare them using ensembles of interaction networks. Investigating the position of specific interactions within the 3D native structure, we developed a parameter-free network descriptor that permits to distinguish thermostable and mesostable proteins with an accuracy of 76% and Area Under the Roc Curve of 78%.

scholarly journals Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome evolution between two wheat cultivars

2018 ◽  
Author(s):  
Anupriya Kaur Thind ◽  
Thomas Wicker ◽  
Thomas Müller ◽  
Patrick M. Ackermann ◽  
Burkhard Steuernagel ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Molecular Mechanisms ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Plant Immunity ◽  
Comparative Sequence Analysis ◽  
Structural Variations ◽  
High Quality ◽  
Evolutionary Mechanisms ◽  
Comparative Sequence

AbstractBackgroundRecent improvements in DNA sequencing and genome scaffolding have paved the way to generate high-quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives. These assemblies form the basis to compare the evolutionary dynamics of wheat genomes on a megabase-scale.ResultsHere, we provide a comparative sequence analysis of the ~700-megabase chromosome 2D between two bread wheat genotypes – the old landrace Chinese Spring and the elite Swiss spring wheat line ‘CH Campala Lr22a’. There was a high degree of sequence conservation between the two chromosomes. Analysis of large structural variations revealed four large insertions/deletions (InDels) of >100 kb. Based on the molecular signatures at the breakpoints, unequal crossing over and double-strand break repair were identified as the evolutionary mechanisms that caused these InDels. Three of the large InDels affected copy number of NLRs, a gene family involved in plant immunity. Analysis of single nucleotide polymorphism (SNP) density revealed three haploblocks of ~8 Mb, ~9 Mb and ~48 Mb with a 35-fold increased SNP density compared to the rest of the chromosome.ConclusionsThis comparative analysis of two high-quality chromosome assemblies enabled a comprehensive assessment of large structural variations. The insight obtained from this analysis will form the basis of future wheat pan-genome studies.

scholarly journals FAM49B promotes breast cancer proliferation, metastasis, and chemoresistance by stabilizing ELAVL1 protein and regulating downstream Rab10/TLR4 pathway

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yanhui Li ◽  
Yue Xiong ◽  
Zhen Wang ◽  
Jianjun Han ◽  
Sufang Shi ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Histological Grade ◽  
Mechanistic Studies ◽  
Gene Interaction Network ◽  
Kaplan Meier ◽  
And Migration ◽  
Proliferation And Migration

Abstract Background Breast cancer (BC) is one of the most common cancers and the leading cause of death in women. Previous studies have demonstrated that FAM49B is implicated in several tumor progression, however, the role and mechanism of FAM49B in BC remain to be explored. Therefore, in this study, we aimed to systematically study the role of FAM49B in the proliferation, metastasis, apoptosis, and chemoresistance of BC, as well as the corresponding molecular mechanisms and downstream target. Methods The ONCOMINE databases and Kaplan–Meier plotter databases were analyzed to find FAM49B and its prognostic values in BC. FAM49B expression in BC and adjacent non-tumor tissues was detected by western blot and IHC. Kaplan–Meier analysis was used to identify the prognosis of BC patients. After FAM49B knockdown in MCF-7 and MDA-MB-231 cells, a combination of co-immunoprecipitation, MTT, migration, and apoptosis assays, nude mouse xenograft tumor model, in addition to microarray detection and data analysis was used for further mechanistic studies. Results In BC, the results showed that the expression level of FAM49B was significantly higher than that in normal breast tissue, and highly expression of FAM49B was significantly positively correlated with tumor volume, histological grade, lymph node metastasis rate, and poor prognosis. Knockdown of FAM49B inhibited the proliferation and migration of BC cells in vitro and in vivo. Microarray analysis revealed that the Toll-like receptor signaling pathway was inhibited upon FAM49B knockdown. In addition, the gene interaction network and downstream protein validation of FAM49B revealed that FAM49B positively regulates BC cell proliferation and migration by promoting the Rab10/TLR4 pathway. Furthermore, endogenous FAM49B interacted with ELAVL1 and positively regulated Rab10 and TLR4 expression by stabilizing ELAVL1. Moreover, mechanistic studies indicated that the lack of FAM49B expression in BC cells conferred more sensitivity to anthracycline and increased cell apoptosis by downregulating the ELAVL1/Rab10/TLR4/NF-κB signaling pathway. Conclusion These results demonstrate that FAM49B functions as an oncogene in BC progression, and may provide a promising target for clinical diagnosis and therapy of BC.

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